From twaddlac at gmail.com Thu Jul 1 10:45:01 2010 From: twaddlac at gmail.com (twaddlac) Date: Thu, 1 Jul 2010 07:45:01 -0700 (PDT) Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? Message-ID: <29046535.post@talk.nabble.com> Hi, I am having a bit of trouble reading in a qual file; I would like to input the qual file into a hash but I can't seem to find a method that returns the qual sequence. Any ideas? Thank you in advance! -- View this message in context: http://old.nabble.com/Read-in-a-Qual-File-like-a-Fasta--tp29046535p29046535.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From rmb32 at cornell.edu Thu Jul 1 20:18:58 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 01 Jul 2010 17:18:58 -0700 Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? In-Reply-To: <29046535.post@talk.nabble.com> References: <29046535.post@talk.nabble.com> Message-ID: <4C2D3072.6080803@cornell.edu> You probably want to do something like: use Bio::SeqIO; my $qual_in = Bio::SeqIO->new( -format => 'qual', -file => $ARGV[0], ); while( my $q = $qual_in->next_seq ) { print "qual for ".$q->id." is: "; print "$_ " for @{ $q->qual }; print "\n"; } twaddlac wrote: > Hi, > > I am having a bit of trouble reading in a qual file; I would like to > input the qual file into a hash but I can't seem to find a method that > returns the qual sequence. Any ideas? Thank you in advance! From cjfields at illinois.edu Fri Jul 2 09:48:19 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 08:48:19 -0500 Subject: [Bioperl-l] BioPerl Switching to GitHub Organization Message-ID: <50D544D2-5F49-482F-9E7F-EB462871B380@illinois.edu> GitHub (as expected) just released their setup for organizations, including open-source projects. The announcement is here: http://github.com/blog/674-introducing-organizations I have already moved bioperl over to an organization account and have added a few co-owners of the github repository. The move is transparent, no one should notice any difference in checking out code. I'm working on reassigning teams to projects at this time, so please post here if there are any problems. chris From iatropoul at gmail.com Fri Jul 2 00:21:09 2010 From: iatropoul at gmail.com (George Iatropoulos) Date: Thu, 1 Jul 2010 21:21:09 -0700 (PDT) Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) Message-ID: Hi guys! I'd like to thank you for this important project. I currently develop a script that uses the SeqIO module to read fasta or files with other bio-formats. However your installation instructions are too difficult to be followed, or even outdated, especially for the mac platform. After trying a week I really can't install bioperl on a Snow Leopard machine (perl 5.10.0) and I tried the CPAN and the fink method. None of them works! Especially cpan seems to mess up with itself and now doesn't install anything! As for the ubuntu platform a simple command like: "sudo apt-get install bioperl" simply does the trick! However I couldn't find this simple command in your installation guidelines, and I don't really understand why I should set up a server, before installing bioperl and then follow this complicated series of instructions, to achieve something that is so simple! I understand that you try to give complete instructions for people who may be pleased with more advanced stuff, but please don't forget biology students who don't have a deep computational background. These guys like me would appreciate some simple stuff to get their job and their projects done, without needing to waste days to figure out complicated-guru stuff. Best wishes and many thanks to all of you because bioperl is really important for us! Georgios Iatropoulos From cjfields at illinois.edu Fri Jul 2 11:46:46 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 10:46:46 -0500 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: References: Message-ID: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > Hi guys! > > I'd like to thank you for this important project. I currently develop > a script that uses the SeqIO module to read fasta or files with other > bio-formats. However your installation instructions are too difficult > to be followed, or even outdated, especially for the mac platform. > > After trying a week I really can't install bioperl on a Snow Leopard > machine (perl 5.10.0) and I tried the CPAN and the fink method. None > of them works! Especially cpan seems to mess up with itself and now > doesn't install anything! That's odd. Can you send me what you are seeing? > As for the ubuntu platform a simple command like: "sudo apt-get > install bioperl" simply does the trick! > However I couldn't find this simple command in your installation > guidelines, and I don't really understand why I should set up a > server, before installing bioperl and then follow this complicated > series of instructions, to achieve something that is so simple! That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > I understand that you try to give complete instructions for people who > may be pleased with more advanced stuff, but please don't forget > biology students who don't have a deep computational background. These > guys like me would appreciate some simple stuff to get their job and > their projects done, without needing to waste days to figure out > complicated-guru stuff. We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > Best wishes and many thanks to all of you because bioperl is really > important for us! > > Georgios Iatropoulos Sorry for the troubles, and thanks for letting us know. Any additional details about installation problems are very welcome. Also, the installation page on the bioperl website is editable (it is a wiki :). So, feel free to add more detail where needed, or use the discussion page to point out problems. chris From steffen_moeller at gmx.de Fri Jul 2 12:39:00 2010 From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=) Date: Fri, 02 Jul 2010 18:39:00 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <4C2E1624.2070402@gmx.de> Hello, On 07/02/2010 05:46 PM, Chris Fields wrote: > On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > > >> Hi guys! >> >> I'd like to thank you for this important project. I currently develop >> a script that uses the SeqIO module to read fasta or files with other >> bio-formats. However your installation instructions are too difficult >> to be followed, or even outdated, especially for the mac platform. >> >> After trying a week I really can't install bioperl on a Snow Leopard >> machine (perl 5.10.0) and I tried the CPAN and the fink method. None >> of them works! Especially cpan seems to mess up with itself and now >> doesn't install anything! >> > That's odd. Can you send me what you are seeing? > > >> As for the ubuntu platform a simple command like: "sudo apt-get >> install bioperl" simply does the trick! >> However I couldn't find this simple command in your installation >> guidelines, and I don't really understand why I should set up a >> server, before installing bioperl and then follow this complicated >> series of instructions, to achieve something that is so simple! >> > That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). > this depends on the age of your distribution rather than on what is apt-get-able from various places. Debian Squeeze has 1.6.1, and so does Ubuntu since Lucid. http://packages.qa.debian.org/b/bioperl.html https://launchpad.net/ubuntu/+source/bioperl > I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > > I am CCing the Debian-Med list just in case they have some better idea here, but what I suggest if you don't want to >> I understand that you try to give complete instructions for people who >> may be pleased with more advanced stuff, but please don't forget >> biology students who don't have a deep computational background. These >> guys like me would appreciate some simple stuff to get their job and >> their projects done, without needing to waste days to figure out >> complicated-guru stuff. >> > We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > The intention of us Debian- and Ubuntu-Helpers is very much also to help you X-core guys to concentrate on whatever you want to concentrate on and by taking as many of the "cannot build this or that" questions away from you as we possibly can. From our point of view, karmic or lenny are already rather ancient. As a BioPerl developer you probably don't want to run any of the packages in your routine anyway, so there is not much of a point to update for you. But I share your concern for production sites that want to sync with your vibrant development. If one wants to stay with binaries I see apt-pinning and backports.org. If one would just add the Debian sources of unstable to the /etc/apt/sources.list, then one could also very easily create distribution-adjusted packages oneself by apt-get source -b bioperl, which would then execute "the make" for you. The original request for a pointer to the Debian/Ubuntu packages would be nice, indeed. We'll see us at BOSC next week. If there is anything you think we should do to help your experience with the distributions then please drop us a line or grep for me in Boston. The segmentation is no problem for the packaging, but possibly more so for the regular user with a biological background. Best, Steffen From kai.blin at biotech.uni-tuebingen.de Sat Jul 3 03:05:26 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Sat, 03 Jul 2010 09:05:26 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <1278140726.2833.77.camel@gonzo.home.kblin.org> On Fri, 2010-07-02 at 10:46 -0500, Chris Fields wrote: Hi Chris, > > As for the ubuntu platform a simple command like: "sudo apt-get > > install bioperl" simply does the trick! > > However I couldn't find this simple command in your installation > > guidelines, and I don't really understand why I should set up a > > server, before installing bioperl and then follow this complicated > > series of instructions, to achieve something that is so simple! > > That's b/c the bioperl that is installed with apt is not up to date. > CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for > bioperl-run (where CPAN is at v.1.6.1). As Steffen already said, the current Ubuntu version is 1.6.1, for both bioperl and bioperl-run. I don't think providing backports for Debian/Ubuntu versions wouldn't be too hard. > I would like to get the releases to a point where they are easily > packaged for apt/yum/ppm/fink/macports/whatever, so any help along > those lines is greatly appreciated. There currently is only an "automated port" of Bioperl on the openSuse Build Service (OBS). I'll probably end up looking into packaging BioPerl for SLES11, and would do that on OBS. Supporting other suse distros is trivial, other RPM-based distros are doable once you figure out the package names. I'd say if Debian, Fedora, Suse and Ubuntu are covered, you're doing pretty fine for Linux. People using more exotic distros will be used to build their own stuff anyway. :) I've got no idea about packaging for OSX. > > I understand that you try to give complete instructions for people who > > may be pleased with more advanced stuff, but please don't forget > > biology students who don't have a deep computational background. These > > guys like me would appreciate some simple stuff to get their job and > > their projects done, without needing to waste days to figure out > > complicated-guru stuff. I think some of the instructions on installing BioPerl are pretty concise and allow you to just copy&paste the commands (see the ubuntu-server install instructions). They might be a bit outdated, I didn't check that. And of course I agree that it would be nicer if you could just point your package manager at the appropriate repository and be done. However, there's only a few people working on BioPerl, and packaging can eat a lot of time, as does keeping install instructions up-to-date. Especially on install instructions, every user can help. Once you wasted days on figuring out the complicated guru-stuff, write a wiki page to explain it in a less complicated way. :) Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From maizemu at gmail.com Sat Jul 3 11:30:14 2010 From: maizemu at gmail.com (Christopher Bottoms) Date: Sat, 3 Jul 2010 10:30:14 -0500 Subject: [Bioperl-l] Fwd: Codefest 2010: Final details In-Reply-To: References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> Message-ID: I will be there first thing Wednesday morning. I'd be glad to help work on any project. On Sat, Jul 3, 2010 at 9:15 AM, Chris Fields wrote: > I will be there on the afternoon of the 7th. There are a couple of > projects one can look into for Moose and Perl 6 (Biome and BioPerl6). I > think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not > sure where that is (might be surplanted by SQLite work?). Would be nice to > talk with Mark re: the wrapper system for BioPerl as well. > > So lots of stuff to think over and plan for. Maybe we should move this to > open-bio-l, or bioperl-l? > > chris (fields) > > On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote: > > > Chris, > > > > I do not have too much experience on cloud computing, either. There > > will be quite a few people from BioPerl . We'll meet and come up with > > a plan first thing in the morning. Unless someone has a very good one > > ready for sharing... > > > > -Heikki > > > > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho > > cell: +966 545 595 849 office: +966 2 808 2429 > > > > Computational Bioscience Research Centre (CBRC), Building #2, Office > #4216 > > 4700 King Abdullah University of Science and Technology (KAUST) > > Thuwal 23955-6900, Kingdom of Saudi Arabia > > > > > > > > > > On 3 July 2010 08:36, Christopher Bottoms wrote: > >> Hi all, > >> > >> I was originally planning on working on cloud computing at the Codefest. > >> However, the 2-day cloud computing tutorial that I was going to attend > in > >> mid June was canceled. Does anyone have any programming that they would > like > >> help with? I have experience with Perl 5, including Moose, and I am > starting > >> to dabble in Perl 6. I have also programmed in Java in the past. I hear > >> Python is easy to learn, so I'd be open to working on a Python project > as > >> well. > >> > >> Thanks, > >> Christopher Bottoms > >> > >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman > wrote: > >>> > >>> Hi all; > >>> Codefest 2010 is finally here: next Wednesday and Thursday at > >>> Harvard Medical School and Massachusetts General Hospital in > >>> beautiful Boston. All of the logistics, directions and details > >>> are on the wiki page: > >>> > >>> http://www.open-bio.org/wiki/Codefest_2010 > >>> > >>> If you want the short version: show up at Harvard Medical School on > >>> Wednesday at 10am and we'll take care of the rest. Thanks to the > >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll > >>> have coffee, lunches and internet. Thanks to Steffen and Ntino, > >>> we'll have Amazon credits to utilize. And of course, there will be > >>> BBQ and drinking on Thursday night when we are finished. > >>> > >>> I'm looking forward to a fun and productive time. The general plan > >>> will be to spend a bit of time on Wednesday morning organizing > >>> ourselves into like minded groups of folks, and then commence with > >>> coding and collaborating. > >>> > >>> If you aren't able to make it and you're listed on the wiki page under > >>> participants, please do cross your name off so we have a good idea of > >>> final numbers. Likewise, if you are coming but haven't put your name up > >>> there please add it. > >>> > >>> If you are interested in helping with making software and data > >>> available on shared cloud resources, here are the latest Amazon > >>> AMIs, snapshots, and the code base: > >>> > >>> Cloud BioLinux images: > >>> 64bit: ami-d62cc4bf > >>> 32bit: ami-5423cb3d > >>> > >>> An EBS public snapshot with indexed genomes: > >>> snap-67446d0f > >>> > >>> Infrastructure: > >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/ > >>> > >>> Send an e-mail with any questions, thoughts or concerns. My phone > >>> number is 617-447-8586 in case you end up hopelessly lost somewhere > >>> in Boston and are desperate to begin programming. > >>> > >>> Looking forward to seeing everyone next Wednesday, > >>> Brad > >> > >> > > From cjfields at illinois.edu Sat Jul 3 14:23:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:23:08 -0500 Subject: [Bioperl-l] Error when Using BLAT???? In-Reply-To: References: Message-ID: <1D738754-1FA5-40CB-B805-27A3A36FF319@illinois.edu> On Jun 29, 2010, at 8:58 AM, Minh Bui wrote: > Hi everyone, > I am writing an application that allows me to search through a database > (yeast.nt*) *with a few queries (yeastquery.fasta). Here is the code: > > *use warnings;* > *use Bio::Tools::Run::Alignment::Blat;* > *use Bio::SeqIO;* > *use Bio::DB::Fasta;* > * * > *my $seqio_object = Bio::SeqIO -> new (-file => > 'C:/Users/MINH/Desktop/yeastquery.fasta', -format => 'fasta'); * > * * > *my $database = 'C:/Users/MINH/Desktop/yeast.nt';* > *my $db = Bio::DB::Fasta->new($database); * > * * > *my $factory = Bio::Tools::Run::Alignment::Blat->new(); * > * > * > *while (my $blat_object = $seqio_object -> next_seq) {** * > * my $results = $factory -> run($blat_object,$db); * > *}* > > > BUT i got this error and don't know how to fix it. I am sorry, i am new to > Perl and Bioperl. I am using window 7, Strawberry. > > > *Replacement list is longer than search list at > C:/strawberry/perl/site/lib/Bio/Range.pm line 251.* > *Use of uninitialized value in concatenation (.) or string at > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm line 251, > line 1.* The above are warnings from perl 5.12 that can be ignored (they have been fixed in bioperl-live on github). > *'-out' is not recognized as an internal or external command,* > *operable program or batch file.* > * > * > *------------- EXCEPTION: Bio::Root::Exception -------------* > *MSG: Blat call ( -out=psl C:\Users\MINH\AppData\Local\Temp\BUiXTGzYC2 > C:\Users\MINH\AppData\Local\Temp\yQK5pzgJ_z) crashed: 256 * > * > * > *STACK: Error::throw* > *STACK: Bio::Root::Root::throw > C:/strawberry/perl/site/lib/Bio/Root/Root.pm:368* > *STACK: Bio::Tools::Run::Alignment::Blat::_run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:261* > *STACK: Bio::Tools::Run::Alignment::Blat::run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:178* > *STACK: D:/eclipswp/bioperl/readfasta.pl:15* > *-----------------------------------------------------------* > > Thank you for your help. That may be a bug; I can check on it (I'm planning on setting up a BLAT pipeline here in the next few days). chris From cjfields at illinois.edu Sat Jul 3 14:27:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:27:32 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: No comments. I'm assuming this is okay to merge into master branch, so will merge in later today. chris On Jun 30, 2010, at 12:35 PM, Chris Fields wrote: > All, > > I have a branch in github (topic/species_proxy) that converts > Bio::Species into a proxy class. This appears to fix a ton of problems > introduced during the Tree/Taxonomy refactoring a few years back. > > Advantages: > > 1) No need for Scalar::Util::weaken within Bio::Species or > Bio::Tree::Node. Cleanup methods are handled during instance > destruction. > > 2) This paves the way a bit more for eventual deprecation of > Bio::Species in 1.7. > > 3) Works with bioperl-db and BioSQL as is (passes on both my local > Ubuntu 9.10 and Mac OS X 10.6), perl 5.10 and 5.12, should work with > earlier perl versions. > > Disadvantages: > > 1) For every Bio::Species, we have a Bio::Taxon, a Bio::Tree::Tree, and > a Bio::DB::Taxonomy (one instance more than the previous Bio::Species > implementation). We can probably reduce that down considerably by > creating the needed instances lazily. > > This fixes: > > bug 3017 use threads to get genbank file error > bug 2594 Bio::Species memory leak > > and possibly others: > > bug 2773 Bio::Tree::Node gets destroyed even though it is still live > > If there are no comments, I'll merge this with the master branch in the > next few days. > > ++++++++++++++++++++++++++++++++++++++++++ > > (NOTE: skip the next two paragraphs if you don't want to read nasty > implementation details) > > Bio::Species had previously inherited from Bio::Taxon, but also required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). > > The above proxy fix converts Bio::Species into a proxy class, which only > inherits the interface (Bio::Tree::NodeI), and delegates to an internal > Bio::Taxon and a Bio::Tree::Tree. Neither contained object has a > reference back to the Bio::Species instance, thus the class can perform > proper garbage collection. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at drycafe.net Sat Jul 3 16:55:30 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 3 Jul 2010 16:55:30 -0400 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > Bio::Species had previously inherited from Bio::Taxon, but also > required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sat Jul 3 19:36:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 18:36:15 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> Message-ID: <57B6FE86-FF5E-4579-B3FB-A2D7AB366117@illinois.edu> On Jul 3, 2010, at 3:55 PM, Hilmar Lapp wrote: > On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > >> Bio::Species had previously inherited from Bio::Taxon, but also required >> it to hold a Bio::Tree::Tree which contained a circular reference back >> to the Bio::Species object, thus requiring Scalar::Util::weaken. This >> has caused several hard-to-diagnose problems with premature garbage >> collection, including some issues with threads (bug 3017). > > > Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? > > -hilmar In my experience, using weaken() is a bit of a 'code smell', and in general there are nice, sane ways to work around it. The solutions I outlined for the SeqI<->SeqFeatureI suggestion I thought made sense, if you think of Bio::SeqI as really more like a Bio::SeqRecord (has-a PrimarySeqI, does hold features, annotations, etc). There are no circular refs in this case: SeqI has-a SeqFeature(s)I, via FeatureHolderI SeqI has-a PrimarySeqI SeqFeatureI has-a PrimarySeqI Nothing refers back to SeqI It's a nice design decision and a great delegation of duties: SeqFeatures shouldn't need the Seq(Record) as a whole but the just the sequence itself, present as the PrimarySeqI, therefore they are attached to that. Any sequence-specific changes (methods, attributes) should therefore be in PrimarySeqI, and if needed could be delegated to for convenience from a relevant SeqI. In this particular instance (Bio::Species), there appeared to be a need to store a ref to the Tree (containing self) in self to implement the prior Bio::Species methods, thus requiring the use of weaken(). To me this was an indication that we really needed to rethink the design of the class. Maybe the containing instance (eg: Bio::Seq in this case) needs to hold the classification (as a Tree) and cache the relevant species NodeI (a Bio::Taxon). As we're still at the stage where we are using a Bio::Species, I pushed that functionality for the time being into the Bio::Species class: it has-a Bio::NodeI and a Bio::Tree::Tree, but neither refers back to the Bio::Species. We're planning on deprecating Bio::Species in future releases anyway, and reimplementing so that Bio::Seq is storing the Tree and the Bio::Taxon species node should be easy when the time comes. Actually, this probably suggests abstracting the simplest parts of that out into a common interface, which could be switched over to Bio::Seq when needed. May work on that a bit... chris From holland at eaglegenomics.com Mon Jul 5 06:06:56 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 5 Jul 2010 11:06:56 +0100 Subject: [Bioperl-l] Job opening at Eagle Message-ID: Hi all - thought this might be of interest to you. ==== Eagle Genomics is 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. With a number of exciting new projects on the horizon we're continuing to build up our team of talented and committed experts to help us deliver them. We are currently looking for a top-class developer to work on a wide range of complex projects. The role involves a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had at least 3 years prior experience developing code for bioinformatics projects. For this Perl/Ensembl role you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. Extensive experience programming in another language, particularly Java, is a bonus but not essential. In addition to your superb technical and customer service skills, you will also: * be able to communicate clearly and proactively, * 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, * be a self-starter and good at managing your own workload and responsibilities. You will also have had hands-on experience in at least two of the following: * SQL query design, * Open-source bioinformatics toolkits such as BioPerl, BioMart, BioSQL, etc., * Amazon EC2, * VMware, * Workflow/pipeline design (preferably using eHive or Taverna), * System and user documentation, * Developing and presenting training courses for users and developers. The successful candidate would be expected to work from our offices near Cambridge. 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. We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. The closing date is 23rd July. ==== cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From davila.marcela at gmail.com Mon Jul 5 08:57:01 2010 From: davila.marcela at gmail.com (Marcela Davila) Date: Mon, 5 Jul 2010 05:57:01 -0700 (PDT) Subject: [Bioperl-l] Infernal parser Message-ID: Hi there! I was wondering where I can set a different program directory (a local directory that has a different version of the Infernal package) rather than that specified in the ENV variable to run cmsearch while using Bio::Tools::Run::Infernal. Thanks! From cjfields at illinois.edu Mon Jul 5 11:19:13 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 10:19:13 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. chris On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > Hi there! > > I was wondering where I can set a different program directory (a local > directory that has a different version of the Infernal package) rather > than that specified in the ENV variable to run cmsearch while using > Bio::Tools::Run::Infernal. > > Thanks! > _______________________________________________ > 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 Jul 5 12:18:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 11:18:30 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: <0A2DAC96-808B-4583-B9F7-DBE44F9F9F86@illinois.edu> Marcela, After taking a look again and running a few local checks, I found that setting INFERNALDIR does work after all. I committed some code so that you can also explicitly set program_dir() as well, so the order of preference is: setting program_dir() > INFERNALDIR > PATH failing if an executable isn't found in any of those. That shouldn't be necessary, though (setting INFERNALDIR in your local env should suffice). Note that the Infernal wrapper only really supports Infernal 1.0 and up now, but the older releases still support pre-1.0 if you need them. chris On Jul 5, 2010, at 10:19 AM, Chris Fields wrote: > Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. > > chris > > On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > >> Hi there! >> >> I was wondering where I can set a different program directory (a local >> directory that has a different version of the Infernal package) rather >> than that specified in the ENV variable to run cmsearch while using >> Bio::Tools::Run::Infernal. >> >> Thanks! >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Tue Jul 6 08:37:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 6 Jul 2010 13:37:05 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl Message-ID: Hello, I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the set of scripts in BioPerl. Below is what I have so far. The script works by reading in a GFF of 'repeat_region's and a fasta file of sequences. It outputs a fasta sequence file with the repeats replaced by Xs. The script clearly needs to be more configurable, but I thought I'd send it along now to see if I'm working along the right lines, or if I should be using a different approach. Comments? Cheers, Dan. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $seq_file; my $gff_file; GetOptions ( "verbose" => \$verbose, "seq=s" => \$seq_file, "gff=s" => \$gff_file, ) or die "failed to parse command line options\n"; die "fail $gff_file : $!\n" unless -s $gff_file; ## Set up the BioPerl objects my $seq_reader = Bio::SeqIO->new( -file => $seq_file, -format => 'fasta' ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => 'fasta', -width => 80 ); my $gff_reader = Bio::FeatureIO->new( -file => $gff_file, -format => 'GFF', ); #warn $seq_reader->width, "\n"; exit; ## Run my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>1){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq 'repeat_region'){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } # Debugging #last if $c > 100; } warn "read $c repeat_region features for ", scalar keys(%repeats), " sequences\n"; ## while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; print length($sequence), "\n" if $verbose > 0; for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, 'X' x ($end - $start)); } print length($sequence), "\n" if $verbose > 0; $seq->seq($sequence); $seq_writer->write_seq($seq); # Debugging; #last; } warn "OK\n"; From armendarez77 at hotmail.com Tue Jul 6 10:23:55 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 07:23:55 -0700 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From sharmashalu.bio at gmail.com Tue Jul 6 10:48:58 2010 From: sharmashalu.bio at gmail.com (shalu sharma) Date: Tue, 6 Jul 2010 10:48:58 -0400 Subject: [Bioperl-l] Intergenomic sequences Message-ID: Hi All, This is not a bioperl question but i thought someone might know the answer. Is there any package/program to find intergenic sequences? I would really appreciate your help. Thanks Shalu From bosborne11 at verizon.net Tue Jul 6 10:36:18 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:36:18 +0200 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: > > Hello, > > I'm designing degenerate primers using > Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 > Ns, but on some sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 6 10:50:25 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:50:25 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: =head1 NAME bioflat_index.pl - index sequence files using Bio::DB::Flat =head1 DESCRIPTION Create or update a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed. =head1 USAGE bioflat_index.pl file1 file2 file3... Options: --create Create or reinitialize the index. If not specified, the index must already exist. --format The format of the sequence files. Must be one of "genbank", "swissprot", "embl" or "fasta". --location Path to the directory in which the index files are stored. --dbname The symbolic name of the database to be created. --indextype Type of index to create. Either "bdb" or "flat". "binarysearch" is the same as "flat". Options can be abbreviated. For example, use -i for --indextype. The following environment variables will be used as defaults if the corresponding options are not provided: OBDA_FORMAT format of sequence file OBDA_LOCATION path to directory in which index files are stored OBDA_DBNAME name of database OBDA_INDEX type of index to create =cut On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > Hello, > > I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the > set of scripts in BioPerl. Below is what I have so far. The script > works by reading in a GFF of 'repeat_region's and a fasta file of > sequences. It outputs a fasta sequence file with the repeats replaced > by Xs. > > The script clearly needs to be more configurable, but I thought I'd > send it along now to see if I'm working along the right lines, or if I > should be using a different approach. > > Comments? > > > Cheers, > Dan. > > > > #!/usr/bin/perl -w > > use strict; > use Getopt::Long; > > use Bio::SeqIO; > use Bio::FeatureIO; > > > > ## Set options > > my $verbose = 0; > my $seq_file; > my $gff_file; > > GetOptions > ( > "verbose" => \$verbose, > "seq=s" => \$seq_file, > "gff=s" => \$gff_file, > ) > or die "failed to parse command line options\n"; > > die "fail $gff_file : $!\n" > unless -s $gff_file; > > > > ## Set up the BioPerl objects > > my $seq_reader = > Bio::SeqIO->new( -file => $seq_file, > -format => 'fasta' > ); > > my $seq_writer = > Bio::SeqIO->new( -fh => \*STDOUT, > -format => 'fasta', > -width => 80 > ); > > my $gff_reader = > Bio::FeatureIO->new( -file => $gff_file, > -format => 'GFF', > ); > > #warn $seq_reader->width, "\n"; exit; > > > > ## Run > > my (%repeats, $c); > > while ( my $feature = $gff_reader->next_feature() ) { > if($verbose>1){ > print > join("\t", #$feature, > $feature->seq_id, > $feature->type->name, > $feature->start, > $feature->end, > ), "\n"; > } > > if($feature->type->name eq 'repeat_region'){ > $c++; > push @{$repeats{ $feature->seq_id }}, > [$feature->start, > $feature->end]; > } > > # Debugging > #last if $c > 100; > } > > warn "read $c repeat_region features for ", > scalar keys(%repeats), " sequences\n"; > > > > ## > > while(my $seq = $seq_reader->next_seq){ > my $id = $seq->id; > my $sequence = $seq->seq; > > print $id, "\n" > if $verbose > 0; > > print length($sequence), "\n" > if $verbose > 0; > > for my $region (@{$repeats{ $id }}){ > my ($start, $end) = @$region; > print "$start\t$end\n" > if $verbose > 1; > > substr($sequence, $start, $end - $start, 'X' x ($end - $start)); > } > > print length($sequence), "\n" > if $verbose > 0; > > $seq->seq($sequence); > > $seq_writer->write_seq($seq); > > # Debugging; > #last; > } > > warn "OK\n"; > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From armendarez77 at hotmail.com Tue Jul 6 11:58:11 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 08:58:11 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: Hi Brian, This sort of worked. The script still dies with the same complaint when the primer sequence is 19 bases long and starts with an 'n': Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't look very DNA to me at .... However, other 19bp long sequences with 3 internal n's are allowed. Is there another way to prevent the script from dying when it comes across these sequences or should I just not allow these sequences to be processed? Thanks, Veronica Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From roy.chaudhuri at gmail.com Tue Jul 6 12:31:04 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 06 Jul 2010 17:31:04 +0100 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: <4C335A48.8000006@gmail.com> Hi Veronica, Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. Cheers. Roy. On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > > Hi Brian, > > This sort of worked. The script still dies with the same complaint > when the primer sequence is 19 bases long and starts with an 'n': > > Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > look very DNA to me at .... > > > However, other 19bp long sequences with 3 internal n's are allowed. > Is there another way to prevent the script from dying when it comes > across these sequences or should I just not allow these sequences to > be processed? > > Thanks, > > Veronica > > Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > > > > Veronica, Yes, when you're making your sequence object do something > like: -alphabet => 'dna' For example: use Bio::Seq; > > $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > PM, wrote: > Hello, > > I'm designing degenerate primers using Bio::Tools::Primer3 and > Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to > catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > Bioperl-l mailing list Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > 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 Jul 6 13:17:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 12:17:03 -0500 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <4C335A48.8000006@gmail.com> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> <4C335A48.8000006@gmail.com> Message-ID: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! chris On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > Hi Veronica, > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > Cheers. > Roy. > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: >> >> Hi Brian, >> >> This sort of worked. The script still dies with the same complaint >> when the primer sequence is 19 bases long and starts with an 'n': >> >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't >> look very DNA to me at .... >> >> >> However, other 19bp long sequences with 3 internal n's are allowed. >> Is there another way to prevent the script from dying when it comes >> across these sequences or should I just not allow these sequences to >> be processed? >> >> Thanks, >> >> Veronica >> >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com >> >> >> >> Veronica, Yes, when you're making your sequence object do something >> like: -alphabet => 'dna' For example: use Bio::Seq; >> >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 >> PM, wrote: >> Hello, >> >> I'm designing degenerate primers using Bio::Tools::Primer3 and >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some >> sequences the script dies with the following error: >> >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't >> look very DNA to me at Perl.pm line 629. >> >> >> >> I couldn't find any information on this error. Is there a way to >> catch or override it? >> >> Thank you, >> >> Veronica >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 6 14:21:10 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 11:21:10 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> References: , ,,<1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , , , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net>, , <4C335A48.8000006@gmail.com>, <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Message-ID: Thank you. The missing 'n' was the problem. Veronica > From: cjfields at illinois.edu > Date: Tue, 6 Jul 2010 12:17:03 -0500 > To: roy.chaudhuri at gmail.com > CC: bioperl-l at lists.open-bio.org; bosborne11 at verizon.net; armendarez77 at hotmail.com > Subject: Re: [Bioperl-l] 85% ATGCN > > Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! > > chris > > On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > > > Hi Veronica, > > > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > > > Cheers. > > Roy. > > > > > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > >> > >> Hi Brian, > >> > >> This sort of worked. The script still dies with the same complaint > >> when the primer sequence is 19 bases long and starts with an 'n': > >> > >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > >> look very DNA to me at .... > >> > >> > >> However, other 19bp long sequences with 3 internal n's are allowed. > >> Is there another way to prevent the script from dying when it comes > >> across these sequences or should I just not allow these sequences to > >> be processed? > >> > >> Thanks, > >> > >> Veronica > >> > >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > >> > >> > >> > >> Veronica, Yes, when you're making your sequence object do something > >> like: -alphabet => 'dna' For example: use Bio::Seq; > >> > >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > >> PM, wrote: > >> Hello, > >> > >> I'm designing degenerate primers using Bio::Tools::Primer3 and > >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > >> sequences the script dies with the following error: > >> > >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > >> look very DNA to me at Perl.pm line 629. > >> > >> > >> > >> I couldn't find any information on this error. Is there a way to > >> catch or override it? > >> > >> Thank you, > >> > >> Veronica > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >> > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From kellert at ohsu.edu Tue Jul 6 17:54:36 2010 From: kellert at ohsu.edu (Tom Keller) Date: Tue, 6 Jul 2010 14:54:36 -0700 Subject: [Bioperl-l] SeqIO tag/location question Message-ID: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Greetings, A genbank file I am working with has features: exon 37167..37302 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=24 exon 39189..39256 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=25 exon 48058..50644 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=26 When I parse it using: my $db = Bio::DB::RefSeq->new(); my $seq = $db->get_Seq_by_acc($accession); my @features = $seq->get_SeqFeatures; for my$feat_obj ( @features ) { if ($feat_obj->primary_tag eq 'exon') { print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; for my $tag ($feat_obj->get_all_tags) { for my $value ($feat_obj->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } } I get the following: primary tag: exon start: 42167 end: 42302 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 24 primary tag: exon start: 44189 end: 44256 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 25 primary tag: exon start: 53058 end: 55644 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 26 Where does the discrepancy in location (+5000) come from? thanks for your help, Tom MMI DNA Services Core Facility 4-2442 kellert at ohsu.edu RJH (CROET/BasicScience) 6339b From cjfields at illinois.edu Tue Jul 6 19:10:18 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 18:10:18 -0500 Subject: [Bioperl-l] SeqIO tag/location question In-Reply-To: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> References: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Message-ID: <0DBD5366-A92B-4A70-B882-7E8FA88A85B0@illinois.edu> RefSeq pulls the file from EBI, not from NCBI (IIRC), so maybe there is a difference between the two versions? Hard to say w/o knowing the exact accession. chris On Jul 6, 2010, at 4:54 PM, Tom Keller wrote: > Greetings, > A genbank file I am working with has features: > exon 37167..37302 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=24 > exon 39189..39256 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=25 > exon 48058..50644 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=26 > > When I parse it using: > my $db = Bio::DB::RefSeq->new(); > my $seq = $db->get_Seq_by_acc($accession); > my @features = $seq->get_SeqFeatures; > for my$feat_obj ( @features ) { > if ($feat_obj->primary_tag eq 'exon') { > print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; > for my $tag ($feat_obj->get_all_tags) { > for my $value ($feat_obj->get_tag_values($tag)) { > print " value: ", $value, "\n"; > } > } > } > } > > I get the following: > primary tag: exon start: 42167 end: 42302 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 24 > primary tag: exon start: 44189 end: 44256 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 25 > primary tag: exon start: 53058 end: 55644 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 26 > > Where does the discrepancy in location (+5000) come from? > > thanks for your help, > Tom > MMI DNA Services Core Facility > 4-2442 > kellert at ohsu.edu > RJH (CROET/BasicScience) 6339b > > > > > > > _______________________________________________ > 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 Tue Jul 6 19:14:15 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 7 Jul 2010 00:14:15 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Cheers Brian! Do you think this script will work if I allow sequence and feature '-format's to be picked by the user among all those listed as valid file formats in BioPerl? http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS Or should I stick to Fasta/GFF (or some other implementation)? Cheers, Dan. On 6 July 2010 15:50, Brian Osborne wrote: > Dan, > > There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: > > =head1 NAME > > bioflat_index.pl - index sequence files using Bio::DB::Flat > > =head1 DESCRIPTION > > ?Create or update a biological sequence database indexed with the > ?Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files > ?containing the sequence information to be indexed. > > =head1 USAGE > > ?bioflat_index.pl file1 file2 file3... > > ?Options: > > ? ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, > ? ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. > > ? ? --format ? ? The format of the sequence files. ?Must be one > ? ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". > > ? ? --location ? ? Path to the directory in which the index files > ? ? ? ? ? ? ? ? ? ? ? ? ? are stored. > > ? ? --dbname ? ? ? The symbolic name of the database to be created. > > ? ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". > ? ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". > > Options can be abbreviated. ?For example, use -i for --indextype. > > The following environment variables will be used as defaults if the > corresponding options are not provided: > > ? ? OBDA_FORMAT ? ? ?format of sequence file > ? ? OBDA_LOCATION ? ?path to directory in which index files are stored > ? ? OBDA_DBNAME ? ? ?name of database > ? ? OBDA_INDEX ? ? ? type of index to create > > =cut > > > On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > >> Hello, >> >> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >> set of scripts in BioPerl. Below is what I have so far. The script >> works by reading in a GFF of 'repeat_region's and a fasta file of >> sequences. It outputs a fasta sequence file with the repeats replaced >> by Xs. >> >> The script clearly needs to be more configurable, but I thought I'd >> send it along now to see if I'm working along the right lines, or if I >> should be using a different approach. >> >> Comments? >> >> >> Cheers, >> Dan. >> >> >> >> #!/usr/bin/perl -w >> >> use strict; >> use Getopt::Long; >> >> use Bio::SeqIO; >> use Bio::FeatureIO; >> >> >> >> ## Set options >> >> my $verbose = 0; >> my $seq_file; >> my $gff_file; >> >> GetOptions >> ?( >> ? "verbose" => \$verbose, >> ? "seq=s" => \$seq_file, >> ? "gff=s" => \$gff_file, >> ?) >> ?or die "failed to parse command line options\n"; >> >> die "fail $gff_file : $!\n" >> ?unless -s $gff_file; >> >> >> >> ## Set up the BioPerl objects >> >> my $seq_reader = >> ?Bio::SeqIO->new( -file => $seq_file, >> ? ? ? ? ? ? ? ? ?-format => 'fasta' >> ? ? ? ? ? ? ? ?); >> >> my $seq_writer = >> ?Bio::SeqIO->new( -fh => \*STDOUT, >> ? ? ? ? ? ? ? ? ?-format => 'fasta', >> ? ? ? ? ? ? ? ? ?-width => 80 >> ? ? ? ? ? ? ? ?); >> >> my $gff_reader = >> ?Bio::FeatureIO->new( -file => $gff_file, >> ? ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >> ? ? ? ? ? ? ? ? ? ?); >> >> #warn $seq_reader->width, "\n"; exit; >> >> >> >> ## Run >> >> my (%repeats, $c); >> >> while ( my $feature = $gff_reader->next_feature() ) { >> ?if($verbose>1){ >> ? ?print >> ? ? ?join("\t", #$feature, >> ? ? ? ? ?$feature->seq_id, >> ? ? ? ? ?$feature->type->name, >> ? ? ? ? ?$feature->start, >> ? ? ? ? ?$feature->end, >> ? ? ? ? ), "\n"; >> ?} >> >> ?if($feature->type->name eq 'repeat_region'){ >> ? ?$c++; >> ? ?push @{$repeats{ $feature->seq_id }}, >> ? ? ?[$feature->start, >> ? ? ? $feature->end]; >> ?} >> >> ?# Debugging >> ?#last if $c > 100; >> } >> >> warn "read $c repeat_region features for ", >> ?scalar keys(%repeats), " sequences\n"; >> >> >> >> ## >> >> while(my $seq = $seq_reader->next_seq){ >> ?my $id = $seq->id; >> ?my $sequence = $seq->seq; >> >> ?print $id, "\n" >> ? ?if $verbose > 0; >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?for my $region (@{$repeats{ $id }}){ >> ? ?my ($start, $end) = @$region; >> ? ?print "$start\t$end\n" >> ? ? ?if $verbose > 1; >> >> ? ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >> ?} >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?$seq->seq($sequence); >> >> ?$seq_writer->write_seq($seq); >> >> ?# Debugging; >> ?#last; >> } >> >> warn "OK\n"; >> _______________________________________________ >> 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 Jul 7 05:42:59 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 07 Jul 2010 11:42:59 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, In my opinion the user should be able to use any supported format as input, yes. Brian O. On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > Cheers Brian! > > Do you think this script will work if I allow sequence and feature > '-format's to be picked by the user among all those listed as valid > file formats in BioPerl? > > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats > http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS > > > Or should I stick to Fasta/GFF (or some other implementation)? > > Cheers, > Dan. > > > On 6 July 2010 15:50, Brian Osborne wrote: >> Dan, >> >> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >> >> =head1 NAME >> >> bioflat_index.pl - index sequence files using Bio::DB::Flat >> >> =head1 DESCRIPTION >> >> Create or update a biological sequence database indexed with the >> Bio::DB::Flat indexing scheme. The arguments are a list of flat files >> containing the sequence information to be indexed. >> >> =head1 USAGE >> >> bioflat_index.pl file1 file2 file3... >> >> Options: >> >> --create Create or reinitialize the index. If not specified, >> the index must already exist. >> >> --format The format of the sequence files. Must be one >> of "genbank", "swissprot", "embl" or "fasta". >> >> --location Path to the directory in which the index files >> are stored. >> >> --dbname The symbolic name of the database to be created. >> >> --indextype Type of index to create. Either "bdb" or "flat". >> "binarysearch" is the same as "flat". >> >> Options can be abbreviated. For example, use -i for --indextype. >> >> The following environment variables will be used as defaults if the >> corresponding options are not provided: >> >> OBDA_FORMAT format of sequence file >> OBDA_LOCATION path to directory in which index files are stored >> OBDA_DBNAME name of database >> OBDA_INDEX type of index to create >> >> =cut >> >> >> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >> >>> Hello, >>> >>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>> set of scripts in BioPerl. Below is what I have so far. The script >>> works by reading in a GFF of 'repeat_region's and a fasta file of >>> sequences. It outputs a fasta sequence file with the repeats replaced >>> by Xs. >>> >>> The script clearly needs to be more configurable, but I thought I'd >>> send it along now to see if I'm working along the right lines, or if I >>> should be using a different approach. >>> >>> Comments? >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> #!/usr/bin/perl -w >>> >>> use strict; >>> use Getopt::Long; >>> >>> use Bio::SeqIO; >>> use Bio::FeatureIO; >>> >>> >>> >>> ## Set options >>> >>> my $verbose = 0; >>> my $seq_file; >>> my $gff_file; >>> >>> GetOptions >>> ( >>> "verbose" => \$verbose, >>> "seq=s" => \$seq_file, >>> "gff=s" => \$gff_file, >>> ) >>> or die "failed to parse command line options\n"; >>> >>> die "fail $gff_file : $!\n" >>> unless -s $gff_file; >>> >>> >>> >>> ## Set up the BioPerl objects >>> >>> my $seq_reader = >>> Bio::SeqIO->new( -file => $seq_file, >>> -format => 'fasta' >>> ); >>> >>> my $seq_writer = >>> Bio::SeqIO->new( -fh => \*STDOUT, >>> -format => 'fasta', >>> -width => 80 >>> ); >>> >>> my $gff_reader = >>> Bio::FeatureIO->new( -file => $gff_file, >>> -format => 'GFF', >>> ); >>> >>> #warn $seq_reader->width, "\n"; exit; >>> >>> >>> >>> ## Run >>> >>> my (%repeats, $c); >>> >>> while ( my $feature = $gff_reader->next_feature() ) { >>> if($verbose>1){ >>> print >>> join("\t", #$feature, >>> $feature->seq_id, >>> $feature->type->name, >>> $feature->start, >>> $feature->end, >>> ), "\n"; >>> } >>> >>> if($feature->type->name eq 'repeat_region'){ >>> $c++; >>> push @{$repeats{ $feature->seq_id }}, >>> [$feature->start, >>> $feature->end]; >>> } >>> >>> # Debugging >>> #last if $c > 100; >>> } >>> >>> warn "read $c repeat_region features for ", >>> scalar keys(%repeats), " sequences\n"; >>> >>> >>> >>> ## >>> >>> while(my $seq = $seq_reader->next_seq){ >>> my $id = $seq->id; >>> my $sequence = $seq->seq; >>> >>> print $id, "\n" >>> if $verbose > 0; >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> for my $region (@{$repeats{ $id }}){ >>> my ($start, $end) = @$region; >>> print "$start\t$end\n" >>> if $verbose > 1; >>> >>> substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>> } >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> $seq->seq($sequence); >>> >>> $seq_writer->write_seq($seq); >>> >>> # Debugging; >>> #last; >>> } >>> >>> warn "OK\n"; >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From gb7 at sanger.ac.uk Wed Jul 7 10:41:13 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Wed, 07 Jul 2010 15:41:13 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes Message-ID: <4C349209.6030209@sanger.ac.uk> Hi. I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? Thanks. Greg. -- 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 heikki.lehvaslaiho at gmail.com Wed Jul 7 13:14:21 2010 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 7 Jul 2010 20:14:21 +0300 Subject: [Bioperl-l] BLAT Howto? In-Reply-To: References: Message-ID: There are BLAT and SSAHA that have been around for some time. For next gen sequences, there are more algorithms coming up all the time. Have a look at e.g. Li and Homer in Briefings in Bioinformatics "A survey of sequence alignment algorithms for next-generation sequencing". -Heikki On 28 June 2010 16:15, Minh Bui wrote: > Hi everyone, > I am new to Bioperl and perl itself and running perl on window 7. > > ?My job is to develop an application that can search through a ?database > with thousands of queries. BLAT is a ?best option (if you know any other > algorithm that can do this, please let me know). I have been searching > through Bioperl BLAT documentation and there is only one document for BLAT > but without example. > I am wondering if anyone has done BLAT using Bioperl, please show me how to > use BLAT in ?Bioperl. > > Thank you very much and sorry for my english. Its not my first language. > _______________________________________________ > 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 Jul 7 22:36:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jul 2010 21:36:22 -0500 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: It is possible our NEXUS parser doesn't do this for some reason, but we would need a sample file to work out the problem. You could try Rutger Vos's Bio::Phylo, which may have this working. chris On Jul 7, 2010, at 9:41 AM, Greg Baillie wrote: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. > > In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. > > Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? > > Thanks. > > Greg. > > > > -- > 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. _______________________________________________ > 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 Jul 8 00:27:56 2010 From: jason at bioperl.org (Jason Stajich) Date: Wed, 07 Jul 2010 21:27:56 -0700 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: <4C3553CC.8030400@bioperl.org> Hi - Is this just that you have internal nodes labeled with the bootstrap/posterior value? If so you just want the node ids for the internal nodes then. The semantics of what is encoded in the internal nodes is not forced by the nexus format so it assumes they are ids by default. You can call $tree->move_id_to_bootstrap to migrate the ids of internal nodes to the bootstrap option. you can also use the -internal_node_id => 'bootstrap' option when initializing TreeIO objects too: =head2 new Title : new Usage : my $obj = Bio::TreeIO->new(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args : a hash. useful keys: -format : Specify the format of the file. Supported formats: newick Newick tree format nexus Nexus tree format nhx NHX tree format svggraph SVG graphical representation of tree tabtree ASCII text representation of tree lintree lintree output format -internal_node_id : what is stored in the internal node ids, bootstrap values or ids, coded as 'bootstrap' or 'id' -jason Greg Baillie wrote, On 7/7/10 7:41 AM: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of > trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I > iterate through the nodes looking for posterior values (/if ( > $node->has_tag('posterior') ) {.../), none of the nodes seem to have > posteriors. > > In fact, none of the nodes have any tags (/my @tags = > $node->get_all_tags(); print join ',', @tags/). And when I dump an > entire tree using Data::Dumper, there is no sign of any of the node > values. > > Does TreeIO handle these values? If so, should I be looking somewhere > other than the tags for the values? > > Thanks. > > Greg. From gb7 at sanger.ac.uk Thu Jul 8 10:24:14 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Thu, 08 Jul 2010 15:24:14 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C3553CC.8030400@bioperl.org> References: <4C349209.6030209@sanger.ac.uk> <4C3553CC.8030400@bioperl.org> Message-ID: <4C35DF8E.1050905@sanger.ac.uk> Hi Jason. I'm trying to get access to the posterior probability value, rate, etc, that are stored within open-square-bracket-ampersand and close-square-bracket ([&]) blocks in the tree string. It appears that this information is stripped out during the parsing of the tree string (I have tried to get it from the $node->bootstrap()). I'm having trouble identifying the module that parses the tree string - I thought I might be able to modify that. Any suggestions where I might find the appropriate code? In the meantime, I'll look at the Bio::Phylo modules (as per Chris' suggestion) to see if they have a way of handling that info. Thanks. Greg. Jason Stajich wrote: > Hi - > > Is this just that you have internal nodes labeled with the > bootstrap/posterior value? If so you just want the node ids for the > internal nodes then. The semantics of what is encoded in the internal > nodes is not forced by the nexus format so it assumes they are ids by > default. > You can call $tree->move_id_to_bootstrap > to migrate the ids of internal nodes to the bootstrap option. > > you can also use the -internal_node_id => 'bootstrap' option when > initializing TreeIO objects too: > > =head2 new > > Title : new > Usage : my $obj = Bio::TreeIO->new(); > Function: Builds a new Bio::TreeIO object > Returns : Bio::TreeIO > Args : a hash. useful keys: > -format : Specify the format of the file. Supported formats: > > newick Newick tree format > nexus Nexus tree format > nhx NHX tree format > svggraph SVG graphical representation of tree > tabtree ASCII text representation of tree > lintree lintree output format > -internal_node_id : what is stored in the internal node ids, > bootstrap values or ids, coded as > 'bootstrap' or 'id' > > -jason > Greg Baillie wrote, On 7/7/10 7:41 AM: >> Hi. >> >> I'm trying to extract information (eg. posterior values) from nodes >> of trees generated using BEAST/treeannotator/FigTree. >> >> The trees, which are in nexus format, seem to load OK, but when I >> iterate through the nodes looking for posterior values (/if ( >> $node->has_tag('posterior') ) {.../), none of the nodes seem to have >> posteriors. >> >> In fact, none of the nodes have any tags (/my @tags = >> $node->get_all_tags(); print join ',', @tags/). And when I dump an >> entire tree using Data::Dumper, there is no sign of any of the node >> values. >> >> Does TreeIO handle these values? If so, should I be looking somewhere >> other than the tags for the values? >> >> Thanks. >> >> Greg. -- 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 dan.bolser at gmail.com Thu Jul 8 10:33:19 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 15:33:19 +0100 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) Message-ID: The bugtracker seems broken (or taking a painfully long time to log me in). So here is my bug report before I forget: Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace Body: The code had inconsistent use of the '_qualify' function, and one instance of a hard-coded table name. These issues were not apparent until "-namespace anything" was used. First I got the fatal error: DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 428, line 2. which was due to a hard-coded table name. Then, after fixing, I got the error: Loading bulk data into database...DBD::mysql::db do failed: Table 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 570, line 10000. i.e. the prefix was being added to the table name twice. I went through the code and tried to make all references to table names consistent to ensure that bugs like this won't creep in again... however, the code for this module isn't very consistent. (See patch attached). -------------- next part -------------- A non-text attachment was scrubbed... Name: mysql.pm.patch Type: text/x-patch Size: 11908 bytes Desc: not available URL: From dan.bolser at gmail.com Thu Jul 8 12:06:59 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 17:06:59 +0100 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) Message-ID: Editing subject to see if it gets through... On 8 July 2010 15:33, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > From lincoln.stein at gmail.com Thu Jul 8 12:24:38 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:24:38 -0400 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) In-Reply-To: References: Message-ID: My code is never very consistent, unfortunately. Thanks for the patch, but it wasn't attached to the forwarded email. Could you try again? Lincoln On Thu, Jul 8, 2010 at 12:06 PM, Dan Bolser wrote: > Editing subject to see if it gets through... > > On 8 July 2010 15:33, Dan Bolser wrote: > > The bugtracker seems broken (or taking a painfully long time to log me > > in). So here is my bug report before I forget: > > > > > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > > > Body: > > The code had inconsistent use of the '_qualify' function, and one > > instance of a hard-coded table name. These issues were not apparent > > until "-namespace anything" was used. > > > > First I got the fatal error: > > > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 428, line 2. > > > > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > > > Loading bulk data into database...DBD::mysql::db do failed: Table > > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 570, line 10000. > > > > > > i.e. the prefix was being added to the table name twice. > > > > > > I went through the code and tried to make all references to table > > names consistent to ensure that bugs like this won't creep in again... > > however, the code for this module isn't very consistent. > > > > (See patch attached). > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform 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 Thu Jul 8 12:28:14 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:28:14 -0400 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) In-Reply-To: References: Message-ID: Never mind. I found the patch in the earlier message. Thanks again for tracking down the issues. Lincoln On Thu, Jul 8, 2010 at 10:33 AM, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From David.Messina at sbc.su.se Thu Jul 8 14:27:13 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jul 2010 14:27:13 -0400 Subject: [Bioperl-l] added -type for Bio::Annotation::DBLink Message-ID: Hi everybody, In working on representing sequence metadata*, I've found it useful to track the type of information that is involved in a database cross-reference. I'm adding an optional -type property to Bio::Annotation::DBLink to support this cleanly in BioPerl. Here follows my rationale. I'm not tied to doing this in B:A::DBLink if there's a better way ? it just seems the best route to me at the moment. -- So, what do I mean by tracking the type of information in a DB crossreference? Right now, a standard DBLink contains database => RefSeq ID => NM_12345 along with a few other optional properties. See the docs for details: http://doc.bioperl.org/bioperl-live/Bio/Annotation/DBLink.html I want to be able to say database => RefSeq ID => NM_12345 type => RNA Why? Two reasons: 1. a single database can store more than one type of information. RefSeq, for example, stores RNA and protein records. Although RefSeq's IDs are named intelligently to note their type (NM_xxx for transcript, NP_xxx for protein), this is not true for all databases and not everybody knows the ID codes. For example, here are three database-ID pairs: Genbank: AK291692.1 Genbank: CH471055.1 Genbank: AAH14616.1 Those are three different record types (mRNA, genomic DNA, protein) from the same database. 2. There can be multiple crossreferences for multiple types of information. There can be multiple source databases providing the same type of crossreference and multiple types of crossreferences. Take this example: Genbank: AAA81779.1 EMBL: AK291692 Ensembl: ENST00000308775 HPA: CAB001960 Two of these are mRNA records, one is a protein record, and one is something else entirely. If I wanted to take one mRNA xref and one protein xref from this set, I couldn't do it using solely the information provided above. If I had type information, though, it'd be easy. And since -type is an optional parameter, it is fully backwards-compatible. Any thoughts or comments? Dave * specifically, in SeqXML. See http://seqxml.org and http://doc.bioperl.org/bioperl-live/Bio/SeqIO/seqxml.html From abhishek.vit at gmail.com Fri Jul 9 11:02:09 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jul 2010 11:02:09 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO Message-ID: Hi (Chris) I feel I might be hitting a bug or missing something. I am trying to convert a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO for more clarity. I think the quality line is missing and the read is breaking into two lines. Any obvious mistakes ? Thanks! -Abhi ## Reading the FASTQ ASCII-64 file my $in = Bio::SeqIO->new( -format => 'fastq', -variant => 'illumina', -file => "<$in_fastq_file", ); ## File Handle for writing ASCII-33 (sanger) standard format my $out = Bio::SeqIO->new ( -format => 'fastq', -variant => 'sanger', -file => ">$out_fastq_file", ); while (my $oneread = $in->next_seq){ $out->write_seq($oneread); } Output: >HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCA AGGATATTGGTCTAA Input: @HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCAAGGATATTGGTCTAA +HWI-EAS397_0006:6:1:1023:19461#0/1 ^aYa^\a^aaaa\]a^^^^^]]]^L^Y]]]aa\`YZ^a]]a[a^^^^^`I^^^`]aaaa]]^]R`W^``^BBBBB From snoze.pa at gmail.com Fri Jul 9 15:06:31 2010 From: snoze.pa at gmail.com (snoze pa) Date: Fri, 9 Jul 2010 14:06:31 -0500 Subject: [Bioperl-l] MSG: Unrecognized DBSOURCE data: pdb: molecule Message-ID: Dear Users, While adding a genebank file to bioperl biosql database i am getting following error. Any Idea or help will be highly appreciated. Thank you s --------------------- WARNING --------------------- MSG: Unrecognized DBSOURCE data: pdb: molecule From biopython at maubp.freeserve.co.uk Sat Jul 10 07:43:47 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:43:47 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: > Hi (Chris) > > I feel I might be hitting a bug or missing something. I am trying to convert > a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO > for more clarity. I think the quality line is missing and the read is > breaking into two lines. > > Any obvious mistakes ? > > Thanks! > -Abhi It looks like you are getting FASTQ out rather than FASTQ (notice in addition to missing the qualities, the record starts with ">" rather than "@". Strange, as you do seem to be using the right FASTQ format and variant names. You could try using format="fastq-sanger" and format="fastq-illumina" rather than setting variant, to see if that changes anything. Peter From biopython at maubp.freeserve.co.uk Sat Jul 10 07:44:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:44:48 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: > On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >> Hi (Chris) >> >> I feel I might be hitting a bug or missing something. I am trying to convert >> a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO >> for more clarity. I think the quality line is missing and the read is >> breaking into two lines. >> >> Any obvious mistakes ? >> >> Thanks! >> -Abhi > > It looks like you are getting FASTQ out rather than FASTQ (notice in addition to > missing the qualities, the record starts with ">" rather than "@". Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) Peter From cjfields at illinois.edu Sat Jul 10 15:23:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jul 2010 14:23:30 -0500 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Jul 10, 2010, at 6:44 AM, Peter wrote: > On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >>> Hi (Chris) >>> >>> I feel I might be hitting a bug or missing something. I am trying to convert >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO >>> for more clarity. I think the quality line is missing and the read is >>> breaking into two lines. >>> >>> Any obvious mistakes ? >>> >>> Thanks! >>> -Abhi >> >> It looks like you are getting FASTQ out rather than FASTQ (notice in addition to >> missing the qualities, the record starts with ">" rather than "@". > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) > > Peter You have to be using a version of BioPerl that supports this. The previous version of the FASTQ parser released prior to refactoring returned FASTA when using write_seq(), which was a significant bug that was fixed during the complete overhaul prior to the FASTQ paper. My guess is the version of BioPerl is old and this is the module version being used. chris PS - Peter, had several very good mentions of this work from all Bio*/EMBOSS talks at BOSC, so a great success! From abhishek.vit at gmail.com Sat Jul 10 16:38:06 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Sat, 10 Jul 2010 16:38:06 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: Thanks guys. Time to update my Bioperl. I will do that and report if I face issues. -A On Sat, Jul 10, 2010 at 3:23 PM, Chris Fields wrote: > On Jul 10, 2010, at 6:44 AM, Peter wrote: > > > On Sat, Jul 10, 2010 at 12:43 PM, Peter > wrote: > >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap > wrote: > >>> Hi (Chris) > >>> > >>> I feel I might be hitting a bug or missing something. I am trying to > convert > >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code > and IO > >>> for more clarity. I think the quality line is missing and the read is > >>> breaking into two lines. > >>> > >>> Any obvious mistakes ? > >>> > >>> Thanks! > >>> -Abhi > >> > >> It looks like you are getting FASTQ out rather than FASTQ (notice in > addition to > >> missing the qualities, the record starts with ">" rather than "@". > > > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close > together ;) > > > > Peter > > You have to be using a version of BioPerl that supports this. The previous > version of the FASTQ parser released prior to refactoring returned FASTA > when using write_seq(), which was a significant bug that was fixed during > the complete overhaul prior to the FASTQ paper. My guess is the version of > BioPerl is old and this is the module version being used. > > chris > > PS - Peter, had several very good mentions of this work from all > Bio*/EMBOSS talks at BOSC, so a great success! From pengyu.ut at gmail.com Sat Jul 10 21:40:47 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sat, 10 Jul 2010 20:40:47 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) Message-ID: Hi, I have the following warnings and perl program. I don't understand why there is a warning and what the error is. The ncbi's eutils url seems OK. If shrink $term (see the code), then the warning is gone. Could somebody let me know what the problem is with my bioperl code? http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 $ ./main.pl |head --------------------- WARNING --------------------- MSG: NCBI esearch Errors/Warnings: Error : --------------------------------------------------- 241 2412410 20616305 20581223 20572313 20564721 20554763 20542744 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::DB::EUtilities; my $factory = Bio::DB::EUtilities->new( -eutil => 'esearch', -db => 'pubmed', -email => 'mymail at foo.bar', #-term => 'anoxia[mh] AND neoplasms[mh]', #-term => 'small ubiquitin-related modifier proteins[mh]', -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR hCaCC-1[tiab]', #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink $term, then the warning is gone. -retmode => 'xml', -retmax => 1000000, ); print $factory->get_retmax,"\n"; print $factory->get_Response->content; -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 11:14:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 10:14:54 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: Message-ID: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > Hi, > > I have the following warnings and perl program. I don't understand why > there is a warning and what the error is. The ncbi's eutils url seems > OK. If shrink $term (see the code), then the warning is gone. Could > somebody let me know what the problem is with my bioperl code? > > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 > > $ ./main.pl |head > > --------------------- WARNING --------------------- > MSG: NCBI esearch Errors/Warnings: > Error : > --------------------------------------------------- > 241 > > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> > 2412410 > 20616305 > 20581223 > 20572313 > 20564721 > 20554763 > 20542744 > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::DB::EUtilities; > > my $factory = Bio::DB::EUtilities->new( > -eutil => 'esearch', > -db => 'pubmed', > -email => 'mymail at foo.bar', > #-term => 'anoxia[mh] AND neoplasms[mh]', > #-term => 'small ubiquitin-related modifier proteins[mh]', > -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] > OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR > hCaCC-1[tiab]', > #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink > $term, then the warning is gone. > -retmode => 'xml', > -retmax => 1000000, > ); > > print $factory->get_retmax,"\n"; > print $factory->get_Response->content; > > > -- > Regards, > Peng The above XML output from that query isn't complete; you left out: CLCRG1[tiab]FLJ95147[tiab] It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. I can take a look, but the error is pretty obvious from that output (can't find those phrases). chris From pengyu.ut at gmail.com Sun Jul 11 15:54:20 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 14:54:20 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 10:14 AM, Chris Fields wrote: > On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > >> Hi, >> >> I have the following warnings and perl program. I don't understand why >> there is a warning and what the error is. The ncbi's eutils url seems >> OK. If shrink $term (see the code), then the warning is gone. Could >> somebody let me know what the problem is with my bioperl code? >> >> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 >> >> $ ./main.pl |head >> >> --------------------- WARNING --------------------- >> MSG: NCBI esearch Errors/Warnings: >> Error : >> --------------------------------------------------- >> 241 >> >> > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> >> 2412410 >> ? ? ? ? ? ? ? 20616305 >> ? ? ? ? ? ? ? 20581223 >> ? ? ? ? ? ? ? 20572313 >> ? ? ? ? ? ? ? 20564721 >> ? ? ? ? ? ? ? 20554763 >> ? ? ? ? ? ? ? 20542744 >> $ cat main.pl >> #!/usr/bin/env perl >> >> use strict; >> use warnings; >> use Bio::DB::EUtilities; >> >> my $factory = Bio::DB::EUtilities->new( >> ?-eutil => 'esearch', >> ?-db => 'pubmed', >> ?-email => 'mymail at foo.bar', >> ?#-term => 'anoxia[mh] AND neoplasms[mh]', >> ?#-term => 'small ubiquitin-related modifier proteins[mh]', >> ?-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] >> OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR >> hCaCC-1[tiab]', >> ?#-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink >> $term, then the warning is gone. >> ?-retmode => 'xml', >> ?-retmax => 1000000, >> ); >> >> print $factory->get_retmax,"\n"; >> print $factory->get_Response->content; >> >> >> -- >> Regards, >> Peng > > The above XML output from that query isn't complete; you left out: > > CLCRG1[tiab]FLJ95147[tiab] > > It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. ?I can take a look, but the error is pretty obvious from that output (can't find those phrases). Is there a way to suppress such error and warning message as they are not interesting to me? (As I can always check how many pubmed ids returned to determine if the search results anything). -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 17:16:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 16:16:15 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > ... > Is there a way to suppress such error and warning message as they are > not interesting to me? (As I can always check how many pubmed ids > returned to determine if the search results anything). > > -- > Regards, > Peng Setting -verbose to -1 should work. chris From pengyu.ut at gmail.com Sun Jul 11 20:04:30 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 19:04:30 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > >> ... >> Is there a way to suppress such error and warning message as they are >> not interesting to me? (As I can always check how many pubmed ids >> returned to determine if the search results anything). >> >> -- >> Regards, >> Peng > > Setting -verbose to -1 should work. I don't see such an option in perldoc Bio::DB::EUtilities. Would you please let me know where it is documented? In fact, I don't see the document for new() in Bio::DB::EUtilities. Would you please add this to the document? Thank you! -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 20:49:37 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 19:49:37 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <98EC5021-C5BC-4568-8080-99AC1C0C95A1@illinois.edu> On Jul 11, 2010, at 7:04 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: >> >> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: >> >>> ... >>> Is there a way to suppress such error and warning message as they are >>> not interesting to me? (As I can always check how many pubmed ids >>> returned to determine if the search results anything). >>> >>> -- >>> Regards, >>> Peng >> >> Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng verbose() is a Bio::Root::Root/RootI method (all BioPerl classes inherit it), so that's the place to look. As for new(), yes I can work on that. chris From Russell.Smithies at agresearch.co.nz Sun Jul 11 21:08:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 13:08:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Take a look at the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities Details all the methods including those that are inherited. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peng Yu > Sent: Monday, 12 July 2010 12:05 p.m. > To: Chris Fields > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields > wrote: > > > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > > > >> ... > >> Is there a way to suppress such error and warning message as they are > >> not interesting to me? (As I can always check how many pubmed ids > >> returned to determine if the search results anything). > >> > >> -- > >> Regards, > >> Peng > > > > Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng > _______________________________________________ > 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 pengyu.ut at gmail.com Sun Jul 11 21:15:46 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 20:15:46 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell wrote: > Take a look at the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > > Details all the methods including those that are inherited. This is every useful when l look for an inherent method. The box titled "methods for Bio::DB::EUtilities" is too small. May I suggest to make it a little bigger? Also, the box above it takes too much space, it is better to shrink it since there in only one class. Would you please help improve the appearance a little? -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 23:45:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 22:45:48 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > wrote: >> Take a look at the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities >> >> Details all the methods including those that are inherited. > > This is every useful when l look for an inherent method. The box > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > to make it a little bigger? Also, the box above it takes too much > space, it is better to shrink it since there in only one class. Would > you please help improve the appearance a little? > > -- > Regards, > Peng Patches welcome chris From Russell.Smithies at agresearch.co.nz Mon Jul 12 00:07:28 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:07:28 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> I think you mean "on your PC the box is too small". Because BioPerl is cross-platform it shouldn't be customized to look best on specific hardware or software , for example, Windows 7 with IE9. The Deobfuscator is included in BioPerl so you are free to edit and run on your own web-server with colors and styles to suit your exacting tastes. And as Chris said, if you'd like added documentation or a web interface changed so it looks better on your PC I suggest you start writing some patches. Don't forget, the BioPerl developers are all volunteers and don't work for you!! --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Monday, 12 July 2010 3:46 p.m. > To: Peng Yu > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > > > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > > wrote: > >> Take a look at the deobfuscator: > >> http://bioperl.org/cgi- > bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&so > rt_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > >> > >> Details all the methods including those that are inherited. > > > > This is every useful when l look for an inherent method. The box > > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > > to make it a little bigger? Also, the box above it takes too much > > space, it is better to shrink it since there in only one class. Would > > you please help improve the appearance a little? > > > > -- > > Regards, > > Peng > > Patches welcome > > chris ======================================================================= 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 Russell.Smithies at agresearch.co.nz Mon Jul 12 00:27:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:27:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347F6@exchsth.agresearch.co.nz> It's all a matter of priorities and I can't see how increasing the number of rows displayed in a web interface is more important than any other items on the list http://www.bioperl.org/wiki/Project_priority_list If you feel strongly about it and you can justify the changes then submit a bug report, and a patch. --Russell > -----Original Message----- > From: Peng Yu [mailto:pengyu.ut at gmail.com] > Sent: Monday, 12 July 2010 4:15 p.m. > To: Smithies, Russell > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 11:07 PM, Smithies, Russell > wrote: > > I think you mean "on your PC the box is too small". > > Because BioPerl is cross-platform it shouldn't be customized to look > best on specific hardware or software , for example, Windows 7 with IE9. > > The Deobfuscator is included in BioPerl so you are free to edit and run > on your own web-server with colors and styles to suit your exacting > tastes. > > > > And as Chris said, if you'd like added documentation or a web interface > changed so it looks better on your PC I suggest you start writing some > patches. > > Don't forget, the BioPerl developers are all volunteers and don't work > for you!! > > This is just a suggestion. Do you think that this is an order? I > didn't mean so. My believe is that if I feel something can be > improved, maybe others think so as well. So I'm make the suggestions > for other users as well. > > You don't have to reply if it can not be done. > > -- > Regards, > Peng ======================================================================= 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 dan.bolser at gmail.com Mon Jul 12 05:34:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 10:34:47 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: OK, here is my final version. I have tested it with GFF / Fasta, and in theory it works with all installed BioPerl sequence / feature file formats, however, I haven't tested any of those. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $feature_file; my $sequence_file; my $feature_format = 'GFF'; my $sequence_format = 'Fasta'; my $feature_to_mask = 'repeat_region'; my $seq_mask_character = 'X'; GetOptions ( "verbose" => \$verbose, "feature_file|f=s" => \$feature_file, "sequence_file|s=s" => \$sequence_file, "feature_format|ff=s" => \$feature_format, "sequence_format|sf=s" => \$sequence_format, "feature_to_mask|m=s" => \$feature_to_mask, "seq_mask_character|c=s" => \$seq_mask_character, ) or die "failed to parse command line options\n"; ## Check options ## A value should be passed die usage() unless $sequence_file && $feature_file; ## The files should exist die "problem with feature file '$feature_file' : $!\n" unless -s $feature_file; die "problem with sequence file '$sequence_file' : $!\n" unless -s $sequence_file; ## The formats should be valid $feature_format = lc($feature_format); die "ERROR: feature format '$feature_format' is not supported!\n\n" unless eval( "require Bio::FeatureIO::$feature_format" ); $sequence_format = lc($sequence_format); die "ERROR: sequence format '$sequence_format' is not supported!\n\n" unless eval( "require Bio::SeqIO::$sequence_format" ); ## Erm... die "1: what are you trying to do?\n" unless $feature_to_mask; die "2: what are you trying to do?\n" unless length($seq_mask_character) == 1; =head1 NAME bp_repeat_mask_sequence.pl - mask sequence features =head1 DESCRIPTION Takes an input sequence file and a feature file, and returns the sequence with 'repeat_region' features masked out (replaced with X's). This is useful for downstream processing of the sequence file. The masked sequence is written to STDOUT. =head1 USAGE bp_repeat_mask_sequence.pl Options: -f --feature_file The file from which the sequence features will be read (for subsequent masking). -s --sequence_file The sequence file (to be masked). --ff --feature_format The format of the feature file (the default is GFF). --sf --sequence_format The format of the sequence file (the default is fasta). -m --feature_to_mask The type of feature to mask (the default is 'repeat_region'). -c --seq_mask_character The 'mask' character to use in the sequence. (the default is 'X'). -v --verbose Generate some debugging output =cut ## Set up the BioPerl objects my $gff_reader = Bio::FeatureIO->new( -file => $feature_file, -format => $feature_format ); my $seq_reader = Bio::SeqIO->new( -file => $sequence_file, -format => $sequence_format, ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => $sequence_format, ); ## Run warn "hashing features to mask\n"; my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>0){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq $feature_to_mask){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } } warn "read $c '$feature_to_mask' features for ", scalar keys(%repeats), " sequences\n"; warn "masking sequences\n"; while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; ## Do the masking for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, $seq_mask_character x ($end - $start) ); } $seq->seq($sequence); $seq_writer->write_seq($seq); } warn "done\n"; # A bit of a hack: sub usage{ `perldoc -T ./$0` } On 7 July 2010 10:42, Brian Osborne wrote: > Dan, > > In my opinion the user should be able to use any supported format as input, yes. > > Brian O. > > On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > >> Cheers Brian! >> >> Do you think this script will work if I allow sequence and feature >> '-format's to be picked by the user among all those listed as valid >> file formats in BioPerl? >> >> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats >> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS >> >> >> Or should I stick to Fasta/GFF (or some other implementation)? >> >> Cheers, >> Dan. >> >> >> On 6 July 2010 15:50, Brian Osborne wrote: >>> Dan, >>> >>> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >>> >>> =head1 NAME >>> >>> bioflat_index.pl - index sequence files using Bio::DB::Flat >>> >>> =head1 DESCRIPTION >>> >>> Create or update a biological sequence database indexed with the >>> Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files >>> containing the sequence information to be indexed. >>> >>> =head1 USAGE >>> >>> bioflat_index.pl file1 file2 file3... >>> >>> Options: >>> >>> ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, >>> ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. >>> >>> ? --format ? ? The format of the sequence files. ?Must be one >>> ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". >>> >>> ? --location ? ? Path to the directory in which the index files >>> ? ? ? ? ? ? ? ? ? ? ? ? are stored. >>> >>> ? --dbname ? ? ? The symbolic name of the database to be created. >>> >>> ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". >>> ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". >>> >>> Options can be abbreviated. ?For example, use -i for --indextype. >>> >>> The following environment variables will be used as defaults if the >>> corresponding options are not provided: >>> >>> ? OBDA_FORMAT ? ? ?format of sequence file >>> ? OBDA_LOCATION ? ?path to directory in which index files are stored >>> ? OBDA_DBNAME ? ? ?name of database >>> ? OBDA_INDEX ? ? ? type of index to create >>> >>> =cut >>> >>> >>> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >>> >>>> Hello, >>>> >>>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>>> set of scripts in BioPerl. Below is what I have so far. The script >>>> works by reading in a GFF of 'repeat_region's and a fasta file of >>>> sequences. It outputs a fasta sequence file with the repeats replaced >>>> by Xs. >>>> >>>> The script clearly needs to be more configurable, but I thought I'd >>>> send it along now to see if I'm working along the right lines, or if I >>>> should be using a different approach. >>>> >>>> Comments? >>>> >>>> >>>> Cheers, >>>> Dan. >>>> >>>> >>>> >>>> #!/usr/bin/perl -w >>>> >>>> use strict; >>>> use Getopt::Long; >>>> >>>> use Bio::SeqIO; >>>> use Bio::FeatureIO; >>>> >>>> >>>> >>>> ## Set options >>>> >>>> my $verbose = 0; >>>> my $seq_file; >>>> my $gff_file; >>>> >>>> GetOptions >>>> ( >>>> "verbose" => \$verbose, >>>> "seq=s" => \$seq_file, >>>> "gff=s" => \$gff_file, >>>> ) >>>> or die "failed to parse command line options\n"; >>>> >>>> die "fail $gff_file : $!\n" >>>> unless -s $gff_file; >>>> >>>> >>>> >>>> ## Set up the BioPerl objects >>>> >>>> my $seq_reader = >>>> Bio::SeqIO->new( -file => $seq_file, >>>> ? ? ? ? ? ? ? ?-format => 'fasta' >>>> ? ? ? ? ? ? ?); >>>> >>>> my $seq_writer = >>>> Bio::SeqIO->new( -fh => \*STDOUT, >>>> ? ? ? ? ? ? ? ?-format => 'fasta', >>>> ? ? ? ? ? ? ? ?-width => 80 >>>> ? ? ? ? ? ? ?); >>>> >>>> my $gff_reader = >>>> Bio::FeatureIO->new( -file => $gff_file, >>>> ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >>>> ? ? ? ? ? ? ? ? ?); >>>> >>>> #warn $seq_reader->width, "\n"; exit; >>>> >>>> >>>> >>>> ## Run >>>> >>>> my (%repeats, $c); >>>> >>>> while ( my $feature = $gff_reader->next_feature() ) { >>>> if($verbose>1){ >>>> ?print >>>> ? ?join("\t", #$feature, >>>> ? ? ? ?$feature->seq_id, >>>> ? ? ? ?$feature->type->name, >>>> ? ? ? ?$feature->start, >>>> ? ? ? ?$feature->end, >>>> ? ? ? ), "\n"; >>>> } >>>> >>>> if($feature->type->name eq 'repeat_region'){ >>>> ?$c++; >>>> ?push @{$repeats{ $feature->seq_id }}, >>>> ? ?[$feature->start, >>>> ? ? $feature->end]; >>>> } >>>> >>>> # Debugging >>>> #last if $c > 100; >>>> } >>>> >>>> warn "read $c repeat_region features for ", >>>> scalar keys(%repeats), " sequences\n"; >>>> >>>> >>>> >>>> ## >>>> >>>> while(my $seq = $seq_reader->next_seq){ >>>> my $id = $seq->id; >>>> my $sequence = $seq->seq; >>>> >>>> print $id, "\n" >>>> ?if $verbose > 0; >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> for my $region (@{$repeats{ $id }}){ >>>> ?my ($start, $end) = @$region; >>>> ?print "$start\t$end\n" >>>> ? ?if $verbose > 1; >>>> >>>> ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>>> } >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> $seq->seq($sequence); >>>> >>>> $seq_writer->write_seq($seq); >>>> >>>> # Debugging; >>>> #last; >>>> } >>>> >>>> warn "OK\n"; >>>> _______________________________________________ >>>> 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 Jul 12 08:42:58 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 13:42:58 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" Message-ID: Seems I still can't log bugs here: https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 Error: Artifact: Only Artifact Admins Can Modify Private ArtifactTypes Here I my bug report: I'm following the tutorial here: http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html I successfully set up and browsed the first database (going no further than #data_file). I decided to try switching from an in memory (file-based) database to a DBI::mysql database. After taking the appropriate steps (see below), I get the following error when viewing the database in GB: The landmark named ctgA is not recognized. See the help pages for suggestions. I'm not sure why the landmark is found using a memory (file-based) database, but not found when using the same GFF loaded into mysql. This is the latest bioperl-live (although I'm still struggling with git). Any hints on what might be going wrong? I've a feeling I should perhaps roll back a few versions, as I noticed some SQL errors coming from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". Cheers, Dan. 1) I loaded the GFF: bp_seqfeature_load.pl -v -v -f -c -z \ --dsn dbi:mysql:mydb:myhost \ --namespace volvox \ --summary \ -u me -p secret \ databases/volvox/volvox_remarks.gff3 2) I changed the volvox.conf file: #db_args = -adaptor memory # -dir '$HTDOCS/databases/volvox' db_args = -adaptor DBI::mysql -dsn mydb:myhost -namespace volvox -user me -pass secret From shalabh.sharma7 at gmail.com Mon Jul 12 10:56:56 2010 From: shalabh.sharma7 at gmail.com (shalabh sharma) Date: Mon, 12 Jul 2010 10:56:56 -0400 Subject: [Bioperl-l] Intergenic regions Message-ID: Hi All, I am trying to find intergenic regions/sequences in genomes. Is there any bioperl module for that ? or any other package/software available? I would really appreciate if anyone can help me out. Thanks Shalabh From awitney at sgul.ac.uk Mon Jul 12 11:37:05 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Mon, 12 Jul 2010 16:37:05 +0100 Subject: [Bioperl-l] Intergenic regions In-Reply-To: References: Message-ID: If the genomes are already annotated then I guess you could just the Bio::Seq modules to pull out the intergenic regions. If there is no annotation yet then you would need to run some kind of gene prediction software first eg Genescan, Glimmer (google will throw up several choices). cheers adam On 12 Jul 2010, at 15:56, shalabh sharma wrote: > Hi All, > I am trying to find intergenic regions/sequences in genomes. Is > there any bioperl module for that ? or any other package/software available? > > I would really appreciate if anyone can help me out. > > Thanks > Shalabh > _______________________________________________ > 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 Jul 12 12:56:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 12 Jul 2010 11:56:12 -0500 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: Message-ID: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Dan. Is this maybe something for the GBrowse list? (cc'ing there JIC) chris On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > --dsn dbi:mysql:mydb:myhost \ > --namespace volvox \ > --summary \ > -u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args = -adaptor memory > # -dir '$HTDOCS/databases/volvox' > > db_args = -adaptor DBI::mysql > -dsn mydb:myhost > -namespace volvox > -user me > -pass secret > _______________________________________________ > 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 Tue Jul 13 03:49:44 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 08:49:44 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: Cheers Chris, Is there a known good version of "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? I believe that this is one of the more common databases, so I'm surprised to find it broken. What would be the git command to roll back to a stable BioPerl / GBrowse? Sorry for the basic questions, Dan. On 12 July 2010 17:56, Chris Fields wrote: > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From mark.alston at BBSRC.AC.UK Tue Jul 13 06:47:04 2010 From: mark.alston at BBSRC.AC.UK (mark alston (TGAC)) Date: Tue, 13 Jul 2010 11:47:04 +0100 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... Message-ID: Hi, BioPerl newbie question coming up... I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. Here's my script after days of effort (I joke not): ######################################################################### use Bio::DB::Taxonomy ; my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects foreach my $nodelet (@taxa) { print $nodelet->to_string() . "\t" ; } ######################################################################### This outputs: 131567 2 1224 1236 91347 543 413496 28141 290339 If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because 2 corresponds to: bacteria (superkingdom) 1224 corresponds to: proteobacteria (phylum) etc etc 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) But how can I get the things I've underlined out via BioPerl? Many thanks, Mark ################################################ Dr Mark Alston, Computer Biologist, The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK. tel +44 (0)1603 450910 e-mail mark.alston at bbsrc.ac.uk web http://www.tgac.bbsrc.ac.uk ################################################ From cjfields at illinois.edu Tue Jul 13 08:58:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jul 2010 07:58:41 -0500 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... In-Reply-To: References: Message-ID: Change to the following: { print $nodelet->scientific_name() . "\t" ; } chris On Jul 13, 2010, at 5:47 AM, mark alston (TGAC) wrote: > Hi, > BioPerl newbie question coming up... > I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. > Here's my script after days of effort (I joke not): > ######################################################################### > use Bio::DB::Taxonomy ; > my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); > > my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; > my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; > > my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects > > foreach my $nodelet (@taxa) > { print $nodelet->to_string() . "\t" ; } > ######################################################################### > > This outputs: > 131567 2 1224 1236 91347 543 413496 28141 290339 > > If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because > 2 corresponds to: bacteria (superkingdom) > 1224 corresponds to: proteobacteria (phylum) > etc etc > 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) > > > But how can I get the things I've underlined out via BioPerl? > Many thanks, > Mark > > ################################################ > Dr Mark Alston, > Computer Biologist, > The Genome Analysis Centre, > Norwich Research Park, > Colney Lane, Norwich, NR4 7UH, UK. > > tel +44 (0)1603 450910 > e-mail mark.alston at bbsrc.ac.uk > web http://www.tgac.bbsrc.ac.uk > ################################################ > > > _______________________________________________ > 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 Tue Jul 13 13:15:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 18:15:02 +0100 Subject: [Bioperl-l] Coordinate converter? Message-ID: Hi, When one sequence exists in the context of another larger sequence (with a precise start, end and strand), what is the easiest way to convert coordinates between the two sequences? I'm guessing there is an object I can load with the appropriate information with a conversion method? However, I'm stuck for details. I have implemented sub-sequences as features, but I'm not sure what to do next. Thanks for any hints, Dan. irc://irc.freenode.net/#bioperl From armendarez77 at hotmail.com Tue Jul 13 14:00:27 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:00:27 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Message-ID: Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From randalls at bioinfo.wsu.edu Tue Jul 13 14:43:35 2010 From: randalls at bioinfo.wsu.edu (randalls at bioinfo.wsu.edu) Date: Tue, 13 Jul 2010 11:43:35 -0700 (PDT) Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: Message-ID: <108709378.25.1279046615031.JavaMail.root@mail> One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Tue Jul 13 14:38:24 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 13 Jul 2010 11:38:24 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <1A4207F8295607498283FE9E93B775B406D676E9@EX02.asurite.ad.asu.edu> And a 64-bit OS and program to be able to utilize greater than 3GB of RAM. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of randalls at bioinfo.wsu.edu Sent: Tuesday, July 13, 2010 11:44 AM To: armendarez77 at hotmail.com Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PI D28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 13 14:57:54 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:57:54 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: That would be nice, but not possible right now :) > Date: Tue, 13 Jul 2010 11:43:35 -0700 > From: randalls at bioinfo.wsu.edu > To: armendarez77 at hotmail.com > CC: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation > > One suggestion is to use a computer with a lot more memory...... > > Randall Svancara > Systems Administrator/DBA/Developer > Main Bioinformatics Laboratory > > > > ----- Original Message ----- > From: armendarez77 at hotmail.com > To: bioperl-l at lists.open-bio.org > Sent: Tuesday, July 13, 2010 11:00:27 AM > Subject: [Bioperl-l] Muscle Alignment and Memory Allocation > > Hello, > > I need to align 20-30 large full genome sequences (150,000+ bp each), > but I run out of memory. I've tried using -maxmb at the command line and > as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either > using it wrong or it's not working. > > I've also tried aligning 2 sequences at a time and then aligning those > alignments using the -profile command, but it's still too much. > > Do you have any advice on how to do such alignments? My attempts are > below. > > Thank you, > > Veronica > > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB > > Alignment not completed, cannot save. > > > > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout > 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.74 MB > > Alignment not completed, cannot save. > > > Using Bio::Tools::Run::Alignment::Muscle and -maxmb > > SCRIPT: my $inputFile = $ARGV[0]; > my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); > > my $alnObj = $factory->align($inputFile); > my $output = "output.clw"; > my $clwOut = Bio::AlignIO->new(-format=>'clustalw', > -file=>">$output.clw"); $clwOut->write_aln($alnObj); > > OUTPUT: > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.9 MB > > Alignment not completed, cannot save. > > --------------------- WARNING --------------------- > MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in > 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] > > --------------------------------------------------- > > > > > > > _________________________________________________________________ The > New Busy is not the too busy. Combine all your e-mail accounts with > Hotmail. > http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 > _______________________________________________ Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From David.Messina at sbc.su.se Tue Jul 13 15:05:16 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jul 2010 15:05:16 -0400 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4B92E3EE-1001-44EE-8D78-B3B05E78A13E@sbc.su.se> I would contact the MUSCLE authors to see what they say, but like Randall said I would suspect that you won't be able to do such a large multiple alignment in 4GB of RAM. Dave From kai.blin at biotech.uni-tuebingen.de Tue Jul 13 14:42:58 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Tue, 13 Jul 2010 20:42:58 +0200 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: Message-ID: <1279046578.2560.14.camel@gonzo.home.kblin.org> On Tue, 2010-07-13 at 11:00 -0700, armendarez77 at hotmail.com wrote: Hi Veronica, > I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. The fact that this also fails on the command line tells me that you're not running into a BioPerl problem. See my comments inline below: [...] > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB ^^^^^^^^^^ [...] > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 ^^^^^^^^^^^^ You're running out of memory at 3211.48 MB, but you're telling muscle it's fine to use 4000 MB. Maybe you might want to provide less memory to -maxmb ..... Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From jason at bioperl.org Tue Jul 13 18:41:24 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:41:24 -0700 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: Message-ID: <4C3CEB94.300@bioperl.org> Bio::Coordinate::Pair? Dan Bolser wrote, On 7/13/10 10:15 AM: > Hi, > > When one sequence exists in the context of another larger sequence > (with a precise start, end and strand), what is the easiest way to > convert coordinates between the two sequences? > > I'm guessing there is an object I can load with the appropriate > information with a conversion method? However, I'm stuck for details. > > I have implemented sub-sequences as features, but I'm not sure what to do next. > > Thanks for any hints, > Dan. > > > irc://irc.freenode.net/#bioperl > _______________________________________________ > 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 Tue Jul 13 18:44:32 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:44:32 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4C3CEC50.6010102@bioperl.org> Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: > That would be nice, but not possible right now :) > > > > >> Date: Tue, 13 Jul 2010 11:43:35 -0700 >> From: randalls at bioinfo.wsu.edu >> To: armendarez77 at hotmail.com >> CC: bioperl-l at lists.open-bio.org >> Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> One suggestion is to use a computer with a lot more memory...... >> >> Randall Svancara >> Systems Administrator/DBA/Developer >> Main Bioinformatics Laboratory >> >> >> >> ----- Original Message ----- >> From: armendarez77 at hotmail.com >> To: bioperl-l at lists.open-bio.org >> Sent: Tuesday, July 13, 2010 11:00:27 AM >> Subject: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> Hello, >> >> I need to align 20-30 large full genome sequences (150,000+ bp each), >> but I run out of memory. I've tried using -maxmb at the command line and >> as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either >> using it wrong or it's not working. >> >> I've also tried aligning 2 sequences at a time and then aligning those >> alignments using the -profile command, but it's still too much. >> >> Do you have any advice on how to do such alignments? My attempts are >> below. >> >> Thank you, >> >> Veronica >> >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3211.48 MB >> >> Alignment not completed, cannot save. >> >> >> >> Using -maxmb at the command line: >> >> $ muscle -in 07-13-2010_fullGenomes.fasta -clwout >> 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.74 MB >> >> Alignment not completed, cannot save. >> >> >> Using Bio::Tools::Run::Alignment::Muscle and -maxmb >> >> SCRIPT: my $inputFile = $ARGV[0]; >> my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); >> >> my $alnObj = $factory->align($inputFile); >> my $output = "output.clw"; >> my $clwOut = Bio::AlignIO->new(-format=>'clustalw', >> -file=>">$output.clw"); $clwOut->write_aln($alnObj); >> >> OUTPUT: >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.9 MB >> >> Alignment not completed, cannot save. >> >> --------------------- WARNING --------------------- >> MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in >> 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] >> >> --------------------------------------------------- >> >> >> >> >> >> >> _________________________________________________________________ The >> New Busy is not the too busy. Combine all your e-mail accounts with >> Hotmail. >> http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 >> _______________________________________________ Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 13 18:48:20 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:48:20 -0700 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: <4C3CED34.9050607@bioperl.org> Dan - I'm not convinced that contig:example is proper type/source for the landmarks & scaffold - i use 'scaffold:chromosome' in my data: What happens if you change the GFF3 file line from ctgA example contig 1 50000 . . . Name=ctgA to ctgA chromosome scaffold 1 50000 . . . Name=ctgA I think this can be tweaked in the config but there may be different defaults for the in memory and DBI::mysql implementation. -jason Dan Bolser wrote, On 7/13/10 12:49 AM: > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >>> Seems I still can't log bugs here: >>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >>> >>> Error: >>> Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >>> >>> >>> Here I my bug report: >>> >>> I'm following the tutorial here: >>> >>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >>> >>> >>> I successfully set up and browsed the first database (going no further >>> than #data_file). I decided to try switching from an in memory >>> (file-based) database to a DBI::mysql database. After taking the >>> appropriate steps (see below), I get the following error when viewing >>> the database in GB: >>> >>> The landmark named ctgA is not recognized. See the help pages >>> for suggestions. >>> >>> >>> I'm not sure why the landmark is found using a memory (file-based) >>> database, but not found when using the same GFF loaded into mysql. >>> >>> This is the latest bioperl-live (although I'm still struggling with git). >>> >>> Any hints on what might be going wrong? I've a feeling I should >>> perhaps roll back a few versions, as I noticed some SQL errors coming >>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> 1) I loaded the GFF: >>> >>> bp_seqfeature_load.pl -v -v -f -c -z \ >>> --dsn dbi:mysql:mydb:myhost \ >>> --namespace volvox \ >>> --summary \ >>> -u me -p secret \ >>> databases/volvox/volvox_remarks.gff3 >>> >>> >>> 2) I changed the volvox.conf file: >>> >>> #db_args = -adaptor memory >>> # -dir '$HTDOCS/databases/volvox' >>> >>> db_args = -adaptor DBI::mysql >>> -dsn mydb:myhost >>> -namespace volvox >>> -user me >>> -pass secret >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 03:38:04 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 09:38:04 +0200 Subject: [Bioperl-l] getting only the aminoacids for a domain Message-ID: Hi, with these lines I download protein sequences matching "jjjj" uniprot code. !/usr/bin/perl use lib '/sw/share/bioperl-pm588'; use Bio::SeqIO; use Bio::DB::SwissProt; $db_obj = Bio::DB::SwissProt->new; $seq_obj = $db_obj->get_Seq_by_id('jjjj'); ...from here, I cut the sequences and get only a piece of each one (with subseq, between j1 and j2 residues) $shortened = $seq_obj->subseq(j1,j2); $seq_obj->seq($shortened); $seqio_obj = Bio::SeqIO->new(-file => '>jjjj.jletra.j1_j2.fasta', -format => 'fasta' ); $seqio_obj->write_seq($seq_obj); How can I download the sequence of ONLY THOSE AMINOACIDS that match, in uniprot, in the Sequence annotation section, Feature key: Domain & Description: lectin, ANK, Sushi,... the name of a given domain ? Is there any way of downloading all the existing fasta sequences for a given domain? Thanks in advance, JR From dan.bolser at gmail.com Wed Jul 14 06:27:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 11:27:02 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <4C3CED34.9050607@bioperl.org> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: Hi Jason, Thanks for the suggestion (see below). On 13 July 2010 23:48, Jason Stajich wrote: > Dan - > I'm not convinced that contig:example is proper type/source for the > landmarks & scaffold - i use 'scaffold:chromosome' in my data: > > What happens if you change the GFF3 file line from > ctgA example contig 1 50000 . . . Name=ctgA > to > ctgA chromosome scaffold 1 50000 . . . Name=ctgA > > > I think this can be tweaked in the config but there may be different > defaults for the in memory and DBI::mysql implementation. I found that this doesn't make any difference, however, I have found more information about what causes the bug. >From my previous email you see that I use bp_seqfeature_load.pl with the "--namespace volvox" option (I should have guessed it was something to do with this). Looking closely at the resulting tables I see that the following tables are empty volvox_attribute volvox_parent2child volvox_feature volvox_interval_stats volvox_name volvox_parent2child they are not empty when created without the "--namespace x" prefix, which is why DBI::mysql 'normally' works. All the other tables: volvox_attributelist volvox_locationlist volvox_meta volvox_sequence volvox_typelist appear to be created correctly, with or without the "--namespace x" prefix. Cheers, Dan. > -jason > Dan Bolser wrote, On 7/13/10 12:49 AM: > > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > > > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > > > > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > ? ? ? ?The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > ?--dsn dbi:mysql:mydb:myhost \ > ?--namespace volvox \ > --summary \ > ?-u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args ? ? ? = -adaptor memory > # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' > > db_args ? ? ? = -adaptor DBI::mysql > ? ? ? ? ? ? ? ?-dsn mydb:myhost > ? ? ? ? ? ? ? ?-namespace volvox > ? ? ? ? ? ? ? ?-user me > ? ? ? ? ? ? ? ?-pass secret > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 06:35:17 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 12:35:17 +0200 Subject: [Bioperl-l] install cpan on mac os x Message-ID: Hi, I have found several problems when installing CPAN in Mac OS X (version 10.6.4) previous to install Bioperl. What's the best choice for installing Bioperl on Mac OS X? I had it installed by using fink, but several modules are not found, I prefer a Unix installation. Is there any trick that I have to bear in mind? Thanks, JR From awitney at sgul.ac.uk Wed Jul 14 08:09:33 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 13:09:33 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: Message-ID: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> I have always found the CPAN route the best way of installing BioPerl on OSX. If you are having problems doing this then try posting any errors and someone may be able to help adam On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > Hi, > I have found several problems when installing CPAN in Mac OS X (version > 10.6.4) previous to install Bioperl. > > What's the best choice for installing Bioperl on Mac OS X? I had it > installed by using fink, but several modules are not found, I prefer a Unix > installation. Is there any trick that I have to bear in mind? > > Thanks, > > JR > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From joseramonblas at gmail.com Wed Jul 14 09:29:53 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 15:29:53 +0200 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix When I do: >perl -MCPAN -e shell cpan> install Bundle::CPAN ...answer Yes to all... and the last lines of my installation are: t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 1. t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 255 tests but ran 2. Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) Result: FAIL Failed 67/85 test programs. 34/9260 subtests failed. make: *** [test_dynamic] Error 255 PMQS/IO-Compress-2.027.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports PMQS/IO-Compress-2.027.tar.gz Running make install make test had returned bad status, won't install without force Failed during this command: ADAMK/File-HomeDir-0.91.tar.gz : make_test NO PMQS/IO-Compress-2.027.tar.gz : make_test NO ...any hint on where my failure comes from is appreciated. More info: Mac OS X 10.4 Xcode developer tools installed Thanks, JR El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on > OSX. > > If you are having problems doing this then try posting any errors and > someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a > Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Jul 14 09:36:45 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 14:36:45 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: <74C17C09-7818-45C9-BD7C-896A74D37F17@sgul.ac.uk> looks like its failing to install PMQS/IO-Compress-2.027.tar.gz. Try installing it on its own cpan> install PMQS/IO-Compress-2.027.tar.gz On 14 Jul 2010, at 14:29, Jos? Ram?n Blas Pastor wrote: > I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > > When I do: > >perl -MCPAN -e shell > cpan> install Bundle::CPAN > > ...answer Yes to all... and the last lines of my installation are: > > t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) > Non-zero exit status: 255 > Parse errors: No plan found in TAP output > t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 29 tests but ran 1. > t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 255 tests but ran 2. > Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) > Result: FAIL > Failed 67/85 test programs. 34/9260 subtests failed. > make: *** [test_dynamic] Error 255 > PMQS/IO-Compress-2.027.tar.gz > /usr/bin/make test -- NOT OK > //hint// to see the cpan-testers results for installing this module, try: > reports PMQS/IO-Compress-2.027.tar.gz > Running make install > make test had returned bad status, won't install without force > Failed during this command: > ADAMK/File-HomeDir-0.91.tar.gz : make_test NO > PMQS/IO-Compress-2.027.tar.gz : make_test NO > > ...any hint on where my failure comes from is appreciated. > > More info: > Mac OS X 10.4 > Xcode developer tools installed > > Thanks, > > JR > > El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on OSX. > > If you are having problems doing this then try posting any errors and someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Wed Jul 14 12:33:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 17:33:47 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <4C3CEB94.300@bioperl.org> References: <4C3CEB94.300@bioperl.org> Message-ID: Brilliant! Thanks Jason. I found the example in the docs a bit confusing, so here is my version (hopefully to be built into an AGP object): #!/usr/bin/perl -w use Bio::Location::Simple; use Bio::Coordinate::Pair; my $ctg = Bio::Location::Simple-> new( -seq_id => 'ctg', -start => 1, -end => 999, -strand => +1 ); my $ctg_on_chr = Bio::Location::Simple-> new( -seq_id => 'chr', -start => 2001, -end => 2999, -strand => -1 ); my $agp = Bio::Coordinate::Pair-> new( -in => $ctg, -out => $ctg_on_chr ); my $match_on_ctg = Bio::Location::Simple-> new( -seq_id => 'hit', -start => 25, -end => 125, -strand => +1 ); print_loc( $agp->map( $match_on_ctg ) ); which gives: "chr 2875 2975 -1" I know the algorithm is simple, but it's not so simple to type it out, base perfect and bug free every time you need it. Cheers, Dan. On 13 July 2010 23:41, Jason Stajich wrote: > Bio::Coordinate::Pair? > > > Dan Bolser wrote, On 7/13/10 10:15 AM: >> >> Hi, >> >> When one sequence exists in the context of another larger sequence >> (with a precise start, end and strand), what is the easiest way to >> convert coordinates between the two sequences? >> >> I'm guessing there is an object I can load with the appropriate >> information with a conversion method? However, I'm stuck for details. >> >> I have implemented sub-sequences as features, but I'm not sure what to do >> next. >> >> Thanks for any hints, >> Dan. >> >> >> irc://irc.freenode.net/#bioperl >> _______________________________________________ >> 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 Jul 14 15:12:20 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jul 2010 13:12:20 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> Message-ID: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> On Jul 14, 2010, at 10:33, Dan Bolser wrote: > I found the example in the docs a bit confusing, Hey Dan, Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Dave From dan.bolser at gmail.com Thu Jul 15 04:42:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 09:42:12 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: On 14 July 2010 20:12, Dave Messina wrote: > > > > > On Jul 14, 2010, at 10:33, Dan Bolser wrote: > >> I found the example in the docs a bit confusing, > > > Hey Dan, > > Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Sure thing Dave. The wiki is my preferred choice because it's easy for me to edit. However, having looked a git a bit, it seems like it should be easy for me to now mod the pod. I've put my code example with comments here: http://bioperl.org/wiki/Module:Bio::Coordinate::Pair One of the main reasons that I gave up editing the wiki is the very slow response time. I'm not sure what the bottleneck could be, but page loads, history checks, open for edits, and saves all take way longer than I'd like. This is especially frustrating when you want to make minor edits. (It may be worth noting that minor edits are the way wikis work [1]). This could be a good opportunity to spam the following conference: NETTAB 2010 - Workshop on biological wikis http://www.nettab.org/2010/ Thanks again for help, Dan. [1] http://www.parc.com/publication/1749/power-of-the-few-vs-wisdom-of-the-crowd.html > Dave > From David.Messina at sbc.su.se Thu Jul 15 10:59:43 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 15 Jul 2010 08:59:43 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> > I've put my code example with comments here: > > http://bioperl.org/wiki/Module:Bio::Coordinate::Pair Great, thanks. Much appreciated. > One of the main reasons that I gave up editing the wiki is the very > slow response time. Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > NETTAB 2010 - Workshop on biological wikis > http://www.nettab.org/2010/ Ah, Naples...love that city. If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. Dave From biopython at maubp.freeserve.co.uk Thu Jul 15 11:41:32 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 16:41:32 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Thu, Jul 15, 2010 at 3:59 PM, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. > BioPerl is a volunteer project and our hosting space is donated. > There were some zombie perl crontab processes were running - Mauricio has killed them and is looking at updating/fixing them. The wiki does seem faster now :) Peter From dan.bolser at gmail.com Thu Jul 15 13:46:45 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 18:46:45 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On 15 July 2010 15:59, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. How big is the wiki database? How about moving to http://bifx.org? >> NETTAB 2010 - Workshop on biological wikis >> http://www.nettab.org/2010/ > > Ah, Naples...love that city. > > If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. > > > Dave From jovel_juan at hotmail.com Thu Jul 15 13:53:04 2010 From: jovel_juan at hotmail.com (Juan Jovel) Date: Thu, 15 Jul 2010 17:53:04 +0000 Subject: [Bioperl-l] How to convert SFF into Fastq Message-ID: Hello! How can I convert a SFF file from 454 into a Fastq format? Thanks a lot! JUAN _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline From biopython at maubp.freeserve.co.uk Thu Jul 15 14:40:05 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 19:40:05 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: > > Hello! > > How can I convert a SFF file from 454 into a Fastq format? > > Thanks a lot! > > JUAN I am aware of three options, none of which use Perl, (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget which), to give you FASTA+QUAL, then using your tool of choice go to FASTQ (e.g. BioPerl). (2) Use the open source command line tool sff_extract (written in Python), it can do FASTA and QUAL, and I think there is an option for FASTQ too. http://bioinf.comav.upv.es/sff_extract/ (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. Things are more complex if you are working with paired end data... Peter From cjfields at illinois.edu Thu Jul 15 15:01:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:01:32 -0500 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Jul 15, 2010, at 12:46 PM, Dan Bolser wrote: > On 15 July 2010 15:59, Dave Messina wrote: >> >>> I've put my code example with comments here: >>> >>> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair >> >> Great, thanks. Much appreciated. >> >> >>> One of the main reasons that I gave up editing the wiki is the very >>> slow response time. >> >> Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > > How big is the wiki database? > > How about moving to http://bifx.org? Depends. We have talked about migrating most (all?) of the most significantly used parts (wiki, blogs) to other sources for a while. The GitHub move also played into that. But this would be a wider OBF-based issue, as it would also involve migrating other OBF-based wikis as well. chris From cjfields at illinois.edu Thu Jul 15 15:04:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:04:15 -0500 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Jul 15, 2010, at 1:40 PM, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter We are planning some tools for SFF work with BioPerl, possibly using BioLib's io_lib bindings. Much of this is to replace the legacy io_lib bindings from bioperl-ext, which is essentially dead at the moment. chris From armendarez77 at hotmail.com Thu Jul 15 15:20:43 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Thu, 15 Jul 2010 12:20:43 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <4C3CEC50.6010102@bioperl.org> References: , <108709378.25.1279046615031.JavaMail.root@mail> , <4C3CEC50.6010102@bioperl.org> Message-ID: Thank you. I'll look into those programs. Veronica Date: Tue, 13 Jul 2010 15:44:32 -0700 From: jason at bioperl.org To: armendarez77 at hotmail.com CC: randalls at bioinfo.wsu.edu; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: That would be nice, but not possible right now :) Date: Tue, 13 Jul 2010 11:43:35 -0700 From: randalls at bioinfo.wsu.edu To: armendarez77 at hotmail.com CC: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 From cjfields at illinois.edu Fri Jul 16 00:38:10 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 23:38:10 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release Message-ID: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> All, After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? chris From dan.bolser at gmail.com Fri Jul 16 03:59:01 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 16 Jul 2010 08:59:01 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: (In theory,) the list of tools that produce and consume SFF can be found here: http://seqwiki.org/SFF Currently listed (and not already mentioned) is: * http://seqwiki.org/PyroBayes On 15 July 2010 19:40, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From chiragmatkarbioinfo at gmail.com Fri Jul 16 11:15:09 2010 From: chiragmatkarbioinfo at gmail.com (chirag matkar) Date: Fri, 16 Jul 2010 20:45:09 +0530 Subject: [Bioperl-l] Perl Web Crawling Message-ID: Hello, My Question Is not based on any Biological Application but in General How can we use Perl extensively in Web Crawling ? -- Regards, Chirag Matkar BTech Bioinformatics From cjfields at illinois.edu Fri Jul 16 11:23:01 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jul 2010 10:23:01 -0500 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <1E0BBB82-C6B4-4351-9133-7E8C4832D252@illinois.edu> http://lmgtfy.com/?q=Perl+Web+crawling chris On Jul 16, 2010, at 10:15 AM, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > > -- > Regards, > Chirag Matkar > BTech Bioinformatics > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From rmb32 at cornell.edu Fri Jul 16 11:23:04 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:04 -0700 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C407958.3010405@cornell.edu> Hi Chirag, This is off-topic for this list, it's not for general Perl questions. Search the CPAN at http://search.cpan.org, there are many modules there that can help you with this. In particular, I would look at WWW::Mechanize. Rob chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From rmb32 at cornell.edu Fri Jul 16 11:23:53 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:53 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: <4C407989.5040609@cornell.edu> My thoughts on this: It sounds like a good plan. Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. So, something to think about going forward. Rob Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From roy.chaudhuri at gmail.com Fri Jul 16 11:24:44 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Fri, 16 Jul 2010 16:24:44 +0100 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C4079BC.5010601@gmail.com> Hi Chirag, This is not an appropriate mailing list for your question, it is intended for discussion of the BioPerl toolkit, not generic bioinformatics or Perl questions. Also, before sending a question to any mailing list you should attempt to answer it yourself. Did you try typing "Perl Web Crawling" into Google? The top few hits look like they may be useful. Cheers, Roy. On 16/07/2010 16:15, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From jun.yin at ucd.ie Fri Jul 16 11:54:36 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Fri, 16 Jul 2010 16:54:36 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign Message-ID: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Dear all, I am the Google Summer of Code student working on refactoring Bio::Align subsystems. The first aim of the project is to recode Bio::SimpleAlign. This is because this package is really useful, but it was created a long time ago, written by several people, and a bit inconsistent mainly due to the above two reasons. I tried to keep the package consistent (e.g. method calling, coding styles) with the previous distribution. However, there are still a few changes. Since this package is created and used by the community, I think it is better to show it to everyone before it is merged with the major distribution. Any suggestions and criticisms are welcome. Here are the major improvements on Bio::SimpleAlign 1. MSA modifying and selection methods are more consistent and easier to use. I have enabled multiple/reverse selections for all sequences/columns selection methods, and change the names to be more understandable. For example, $aln->select() and $aln->select_noncont() are both deprecated, and renamed as $aln->select_Seqs() now. Because selections should be both in seqs and columns, which need to be explicit in the method call. For example, multiple sequence selections can be called by: $newaln=$aln->select_Seqs([4..10,20..35,37]); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37]); Or you can toggle selection(reverse selection) using: $newaln=$aln->select_Seqs([4..10,20..35,37],1); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37],-toggle=>1); If you can the method using the old ways, e.g. $newaln=$aln->select(1,5); A warning will be shown: select - deprecated method. Use select_Seqs() instead. And, the calling will be redirected to $newaln=$aln->select_Seqs([1..5]); 2. gap chars/missing chars are more consistent in the package Default values for gap char and missing char are now set in the package. Calling/Setting gap char should be made by calling $aln->gap_char("-"). 3. Some redundant methods are removed. The methods are moved to more reasonable categories. For example, $aln->select and $aln->select_noncont are deprecated now. Please use $aln->select_Seqs. 4. Some methods are renamed. Methods selecting/giving objects are capitalized, e.g. each_seq to each_Seq. Another example, the method is renamed to give a clearer information. $aln->purge is renamed into $aln->remove_redundant_Seqs $aln->splice_by_seq_pos is renamed to $aln->remove_gaps For further information, you can visit: http://spreadsheets.google.com/ccc?key=0AssLTcJFJMbXdDFfZGpJZlhidFY5blBneGdh QUZ6WFE &hl=en&authkey=CJTCw4QL Cheers, Jun Yin Ph.D. student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin From dan.bolser at gmail.com Fri Jul 16 19:15:03 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 17 Jul 2010 00:15:03 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: On 14 July 2010 11:27, Dan Bolser wrote: > Hi Jason, > > Thanks for the suggestion (see below). > > On 13 July 2010 23:48, Jason Stajich wrote: >> Dan - >> I'm not convinced that contig:example is proper type/source for the >> landmarks & scaffold - i use 'scaffold:chromosome' in my data: >> >> What happens if you change the GFF3 file line from >> ctgA example contig 1 50000 . . . Name=ctgA >> to >> ctgA chromosome scaffold 1 50000 . . . Name=ctgA >> >> >> I think this can be tweaked in the config but there may be different >> defaults for the in memory and DBI::mysql implementation. > > I found that this doesn't make any difference, however, I have found > more information about what causes the bug. > > From my previous email you see that I use bp_seqfeature_load.pl with > the "--namespace volvox" option (I should have guessed it was > something to do with this). Looking closely at the resulting tables I > see that the following tables are empty > > volvox_attribute > volvox_parent2child > volvox_feature > volvox_interval_stats > volvox_name > volvox_parent2child > > > they are not empty when created without the "--namespace x" prefix, > which is why DBI::mysql 'normally' works. > > All the other tables: > > volvox_attributelist > volvox_locationlist > volvox_meta > volvox_sequence > volvox_typelist > > > appear to be created correctly, with or without the "--namespace x" prefix. It might be worth mentioning that this issue can be 'resolved' by not using the -f (fast load) option. i.e. its the specific combination of --namespace and -f that causes the bug. http://bugzilla.open-bio.org/show_bug.cgi?id=3110 > Cheers, > Dan. > >> -jason >> Dan Bolser wrote, On 7/13/10 12:49 AM: >> >> Cheers Chris, >> >> Is there a known good version of >> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? >> I believe that this is one of the more common databases, so I'm >> surprised to find it broken. >> >> What would be the git command to roll back to a stable BioPerl / GBrowse? >> >> >> Sorry for the basic questions, >> Dan. >> >> On 12 July 2010 17:56, Chris Fields wrote: >> >> >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >> >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > From bernd.web at gmail.com Sat Jul 17 08:21:46 2010 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 17 Jul 2010 14:21:46 +0200 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: Dear Jun, Thanks for your work on this. Just a few remarks. -is changing methods names indeed needed? this will break existing code (for some time) -i am not sure how naming is generally done now in BioPerl, but is used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has an "_" followed by a capital. I'd stick with each_seq like names. You now changed it too "each_Seq" but gap_char for example remained gap_char. But surely others know better how/if to change naming. > 2. gap chars/missing chars are more consistent in the package > Default values for gap char and missing char are now set in the package. > Calling/Setting gap char should be made by calling $aln->gap_char("-"). So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char. > Another example, the method is renamed to give a clearer information. > > $aln->purge is renamed into $aln->remove_redundant_Seqs Purge to me is a clear name in aln context ;-) > $aln->splice_by_seq_pos is renamed to $aln->remove_gaps But there was already a remove_gaps method. $aln2 = $aln->remove_gaps Function : Creates an aligment with gaps removed Title : splice_by_seq_pos Usage : $status = splice_by_seq_pos(1); Function: splices all aligned sequences where the specified sequence has gaps. So remove_gaps now takes an optional argument to indicate a 'reference' sequence for splicing? Cheers, Bernd From cjfields at illinois.edu Sat Jul 17 13:07:50 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 12:07:50 -0500 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: On Jul 17, 2010, at 7:21 AM, Bernd Web wrote: > Dear Jun, > > Thanks for your work on this. > Just a few remarks. > -is changing methods names indeed needed? this will break existing > code (for some time) There is expected to be a standard deprecation cycle along with this. Changes would not be merged in until after the 1.6.2 release. > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has > an "_" followed by a capital. I'd stick with each_seq like names. You > now changed it too "each_Seq" but gap_char for example remained > gap_char. But surely others know better how/if to change naming. Technically, we would like to standardize that when object(s) are returned (such as each_seq and it's previous incarnations) the method would have the class in caps, whereas simple data would not. There have been several starts along this path, but I think various methods (next_seq in SeqIO being one) still haven't changed. Also, just to point out, it's not terribly hard to alias these as needed: *eachSeq = \&each_Seq; >> 2. gap chars/missing chars are more consistent in the package >> Default values for gap char and missing char are now set in the package. >> Calling/Setting gap char should be made by calling $aln->gap_char("-"). > So the change here is that now the default values are actually set in > new, instead of setting a the default by calling gap_char. Maybe Jun could answer this, but to me this one makes sense (methods like this, which are relied upon for various reaons, need defaults for proper state). '-' is the most commonly-used symbol. >> Another example, the method is renamed to give a clearer information. >> >> $aln->purge is renamed into $aln->remove_redundant_Seqs > Purge to me is a clear name in aln context ;-) Possibly. However alignments can hold more than sequence data (stockholm format, for example), so maybe purge() on it's own is not descriptive enough. Jun, is remove_redundant_Seqs() an alias/reimplementation for purge()? The name might be a little misleading. >> $aln->splice_by_seq_pos is renamed to $aln->remove_gaps > But there was already a remove_gaps method. > $aln2 = $aln->remove_gaps > Function : Creates an aligment with gaps removed > > Title : splice_by_seq_pos > Usage : $status = splice_by_seq_pos(1); > Function: splices all aligned sequences where the specified sequence > has gaps. > > So remove_gaps now takes an optional argument to indicate a > 'reference' sequence for splicing? > > > Cheers, > Bernd This one I'm not sure about, as the two methods to me seem unrelated from name alone. Jun? chris From cjfields at illinois.edu Sun Jul 18 00:23:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 23:23:49 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <4C407989.5040609@cornell.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> <4C407989.5040609@cornell.edu> Message-ID: On Jul 16, 2010, at 10:23 AM, Robert Buels wrote: > My thoughts on this: > > It sounds like a good plan. > > Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Precisely. > Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. > > If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. > > So, something to think about going forward. > > Rob I mentioned this at BOSC (it's briefly touched upon in the talk); it was agreed that the bottom-up approach is the best. Basically, if we can somehow emulate the larger distribution by allowing installation of the various packages then it makes life much easier for users, just have to decide what is the best approach. chris From rondonbio at yahoo.com.br Sun Jul 18 07:55:44 2010 From: rondonbio at yahoo.com.br (Rondon Neto) Date: Sun, 18 Jul 2010 04:55:44 -0700 (PDT) Subject: [Bioperl-l] Jaccard Dendrogram Message-ID: <750495.60162.qm@web63703.mail.re1.yahoo.com> Hi! Please, can I build a dendrogram from a jaccard distance matrix by Phylogenetic Analysis Pipeline? How to do that? Thank you Rondon From hlapp at drycafe.net Sun Jul 18 10:26:34 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 18 Jul 2010 10:26:34 -0400 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <89E90610-355B-4568-BFE2-301B7F4A7E61@drycafe.net> On Jul 17, 2010, at 8:21 AM, Bernd Web wrote: > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq" each_XXX is the old convention, which we aimed to deprecate before 1.4.x, in fact. Maybe we haven't swept through the entire codebase, but where we can we should certain change it. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From David.Messina at sbc.su.se Sun Jul 18 13:26:52 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 18 Jul 2010 11:26:52 -0600 Subject: [Bioperl-l] Jaccard Dendrogram In-Reply-To: <750495.60162.qm@web63703.mail.re1.yahoo.com> References: <750495.60162.qm@web63703.mail.re1.yahoo.com> Message-ID: Hi Rondon, No, I don't think BioPerl has the ability to do Jaccard distance calculations. Looks like SciPy-cluster can, though: http://code.google.com/p/scipy-cluster/ Also MATLAB probably. However, if you or anyone ese should be so inclined, it should be straightforward to adapt one of the existing BioPerl distance methods. See e.g. Bio::Align::DNAStatistics: http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html Dave On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > Hi! Please, can I build a dendrogram from a jaccard distance matrix by > Phylogenetic Analysis Pipeline? > How to do that? > > Thank you > > Rondon > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From florent.angly at gmail.com Mon Jul 19 04:47:39 2010 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 19 Jul 2010 18:47:39 +1000 Subject: [Bioperl-l] New Bio::Root::IO->_insert() method Message-ID: <4C44112B.1060701@gmail.com> Hi list, I needed a feature to insert text at an arbitrary line in a file for a Bioperl module I am working on. I coded it, called the new method _insert( ) and added it to the Bio::Root::IO module because I realized that it could be useful to other Bioperl modules. The method seems to be working well and does not cause tests to fail but let me know if you encounter issues with it. Regards, Florent From jun.yin at ucd.ie Mon Jul 19 06:43:50 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Mon, 19 Jul 2010 11:43:50 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <004c01cb272f$4626b880$d2742980$%yin@ucd.ie> Hi, Thx for all your comments. 1. About each_seq(each_Seq) As Chris Fields says, we tend to capitalize the method name which returns objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so it is better to use a capitalized name as each_Seq. But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because it may be confused with the each() function in Core. So it may need to be renamed to next_Seq eventually. Usually, what I do for the old method is: sub each_seq { my $self = shift; $self->deprecated("each_seq - deprecated method. Use each_Seq() instead."); $self->each_Seq(); } Thus, if you call the old method, it will still continue to run, but give a deprecated warning. This is done on all deprecated methods. 2. To Bernd Web, " So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char." Yes, gap_char has a default value "-" now, so is missing_char "?" and match_char ".". 3. To Bernd Web and Chris Fields, remove_redundant_Seqs() is just an alias for purge(). However, splice_by_seq_pos() is reimplemented and merged with the old remove_gaps(), because these two methods are actually doing similar things. The new remove_gaps() is: Title : remove_gaps Usage : $aln2 = $aln->remove_gaps(-reference=>5) Function : Creates an aligment with gaps removed Returns : a Bio::SimpleAlign object Args : -GAPCHAR a gap character(optional) if none specified taken from $self->gap_char, -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) indicates that only all-gaps columns should be deleted -REFERENCE splices all aligned sequences where the specified sequence has gaps. If you call the old splice_by_seq_pos(), it will be redirected to remove_gaps() by: sub splice_by_seq_pos{ my $self = shift; $self->deprecated("splice_by_seq_pos - deprecated method. Use remove_gaps() instead."); $self->remove_gaps(-reference=>$_[0]); } When I finally finish the recoding for Bio::SimpleAlign, I will write an online HOWTO. Plus, I think I will include an update log, to show which method is renamed and which is reimplemented, thus to make things clearer. Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin __________ Information from ESET Smart Security, version of virus signature database 5291 (20100719) __________ The message was checked by ESET Smart Security. http://www.eset.com From kellert at ohsu.edu Mon Jul 19 13:05:24 2010 From: kellert at ohsu.edu (Tom Keller) Date: Mon, 19 Jul 2010 10:05:24 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 20 In-Reply-To: References: Message-ID: Greetings, R has a jaccard function also. See http://pbil.univ-lyon1.fr/library/prabclus/html/jaccard.html for a description. cheers, Thomas (Tom) Keller, PhD kellert at ohsu.edu 503.494.2442 6339b R Jones Hall (BSc/CROET) www.ohsu.edu/xd/research/research-cores/dna-analysis/ On Jul 19, 2010, at 9:00 AM, wrote: > Send Bioperl-l mailing list submissions to > bioperl-l at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/bioperl-l > or, via email, send a message with subject or body 'help' to > bioperl-l-request at lists.open-bio.org > > You can reach the person managing the list at > bioperl-l-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioperl-l digest..." > > > Today's Topics: > > 1. Re: Jaccard Dendrogram (Dave Messina) > 2. New Bio::Root::IO->_insert() method (Florent Angly) > 3. Re: Recoding Bio::SimpleAlign (Jun Yin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 18 Jul 2010 11:26:52 -0600 > From: Dave Messina > Subject: Re: [Bioperl-l] Jaccard Dendrogram > To: Rondon Neto > Cc: bioperl-l at lists.open-bio.org > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Hi Rondon, > > No, I don't think BioPerl has the ability to do Jaccard distance > calculations. Looks like SciPy-cluster can, though: > > http://code.google.com/p/scipy-cluster/ > > Also MATLAB probably. > > However, if you or anyone ese should be so inclined, it should be > straightforward to adapt one of the existing BioPerl distance methods. See > e.g. Bio::Align::DNAStatistics: > > http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html > > > > > Dave > > > > > > On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > >> Hi! Please, can I build a dendrogram from a jaccard distance matrix by >> Phylogenetic Analysis Pipeline? >> How to do that? >> >> Thank you >> >> Rondon >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > ------------------------------ > > Message: 2 > Date: Mon, 19 Jul 2010 18:47:39 +1000 > From: Florent Angly > Subject: [Bioperl-l] New Bio::Root::IO->_insert() method > To: bioperl-l BioPerl > Message-ID: <4C44112B.1060701 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi list, > I needed a feature to insert text at an arbitrary line in a file for a > Bioperl module I am working on. I coded it, called the new method > _insert( ) and added it to the Bio::Root::IO module because I realized > that it could be useful to other Bioperl modules. The method seems to be > working well and does not cause tests to fail but let me know if you > encounter issues with it. > Regards, > Florent > > > ------------------------------ > > Message: 3 > Date: Mon, 19 Jul 2010 11:43:50 +0100 > From: Jun Yin > Subject: Re: [Bioperl-l] Recoding Bio::SimpleAlign > To: "'Bernd Web'" > Cc: bioperl-l at lists.open-bio.org, 'Chris Fields' > , bernd.web at gmail.com > Message-ID: <004c01cb272f$4626b880$d2742980$%yin at ucd.ie> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > Thx for all your comments. > > 1. About each_seq(each_Seq) > As Chris Fields says, we tend to capitalize the method name which returns > objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so > it is better to use a capitalized name as each_Seq. > But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because > it may be confused with the each() function in Core. So it may need to be > renamed to next_Seq eventually. > > Usually, what I do for the old method is: > > sub each_seq { > my $self = shift; > $self->deprecated("each_seq - deprecated method. Use each_Seq() > instead."); > $self->each_Seq(); > } > > Thus, if you call the old method, it will still continue to run, but give a > deprecated warning. This is done on all deprecated methods. > > > 2. To Bernd Web, " So the change here is that now the default values are > actually set in new, instead of setting a the default by calling gap_char." > > Yes, gap_char has a default value "-" now, so is missing_char "?" and > match_char ".". > > 3. To Bernd Web and Chris Fields, > remove_redundant_Seqs() is just an alias for purge(). > However, splice_by_seq_pos() is reimplemented and merged with the old > remove_gaps(), because these two methods are actually doing similar things. > The new remove_gaps() is: > > Title : remove_gaps > Usage : $aln2 = $aln->remove_gaps(-reference=>5) > Function : Creates an aligment with gaps removed > Returns : a Bio::SimpleAlign object > Args : -GAPCHAR a gap character(optional) if none specified taken > from $self->gap_char, > -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) > indicates that only all-gaps columns should be deleted > -REFERENCE splices all aligned sequences where the specified > sequence has gaps. > > If you call the old splice_by_seq_pos(), it will be redirected to > remove_gaps() by: > sub splice_by_seq_pos{ > my $self = shift; > $self->deprecated("splice_by_seq_pos - deprecated method. Use > remove_gaps() instead."); > $self->remove_gaps(-reference=>$_[0]); > } > > When I finally finish the recoding for Bio::SimpleAlign, I will write an > online HOWTO. > Plus, I think I will include an update log, to show which method is renamed > and which is reimplemented, thus to make things clearer. > > Cheers, > Jun Yin > Ph.D.?student in U.C.D. > > Bioinformatics Laboratory > Conway Institute > University College Dublin > > > > __________ Information from ESET Smart Security, version of virus signature > database 5291 (20100719) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > > > > > > ------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > End of Bioperl-l Digest, Vol 87, Issue 20 > ***************************************** From jonathan at leto.net Mon Jul 19 18:59:27 2010 From: jonathan at leto.net (Jonathan Leto) Date: Mon, 19 Jul 2010 15:59:27 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: Howdy, I recently found a bug in parsing InterPro XML, which I have created a bug for, as well as patches which fix the problem with a test case: http://bugzilla.open-bio.org/show_bug.cgi?id=3121 I would very much like to get feedback on this patch and have it included in the next 1.6.x release. Thanks, Duke On Thu, Jul 15, 2010 at 9:38 PM, Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. ?This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. ?That will be followed by releases of the run, db, and network distributions. ?Any other thoughts? ?Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jonathan "Duke" Leto jonathan at leto.net http://leto.net From jay at jays.net Mon Jul 19 18:24:05 2010 From: jay at jays.net (Jay Hannah) Date: Mon, 19 Jul 2010 17:24:05 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <9331AD17-C3FB-47E9-80C3-2D1360E9EC8C@jays.net> Greetings, I opened bug 3120 today. Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? http://bugzilla.open-bio.org/show_bug.cgi?id=3120 http://bugzilla.open-bio.org/attachment.cgi?id=1526 Or maybe it's just me? :) Thanks, Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From ycchen1981 at gmail.com Mon Jul 19 23:47:45 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Tue, 20 Jul 2010 11:47:45 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.abi format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my $in = Bio::SeqIO->new(-file => "$inputfilename", -format => 'abi'); my $out = Bio::SeqIO->new(-file => ">$outputfilename", -format => 'phd'); while ( my $seq = $in->next_seq() ) { for my $curr(1 .. $seq->length()) { print "[",$seq->qualat($curr),"]:"; print "[",$seq->trace_index_at($curr),"]\t"; } $out->write_seq($seq); last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From Jonathan_Epstein at nih.gov Tue Jul 20 13:53:00 2010 From: Jonathan_Epstein at nih.gov (Jonathan Epstein) Date: Tue, 20 Jul 2010 13:53:00 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? Message-ID: <4C45E27C.9090400@nih.gov> Hi, I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. Then there's the small matter of loading the hg18 annotations into the appropriate relational database. Thanks in advance for your guidance, Jonathan From rmb32 at cornell.edu Tue Jul 20 14:42:36 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 20 Jul 2010 11:42:36 -0700 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <4C45EE1C.7080401@cornell.edu> Take a look at Bio::DB::SeqFeature::Store. It's got a loader that ships with bioperl, bp_seqfeature_load.pl. perldoc Bio::DB::SeqFeature::Store. From the sound of it, the GMOD/Chado stuff might be too heavyweight for what you are doing. But a good method for accessing a Chado schema from Perl is Bio::Chado::Schema, http://search.cpan.org/perldoc?Bio::Chado::Schema, which is based on DBIx::Class. Hope this helps! Rob Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features > associated with a particular genomic region in the hg18 human assembly. > This seems to require a relational database. Of course I would like to > do this using Bioperl. > > So then the question becomes: what's the best approach to use? > Biosql/BioPerl-db looks like the cleanest solution, but it's not clear > to me how up-to-date it is; it sort of looks like an abandoned project. > > CHADO/Gmod is more actively maintained, but I don't know how/whether I > can obtain BioPerl bindings. > > I am also open to using the UCSC databases as a starting point, since > I've already mirrored most of the human-related portions of the UCSC > environment. > > > Then there's the small matter of loading the hg18 annotations into the > appropriate relational database. > > > Thanks in advance for your guidance, > > Jonathan > > > > > > _______________________________________________ > 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 Jul 20 14:55:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jul 2010 13:55:15 -0500 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <827D02E9-9AA8-4474-BBA4-FC15BAAC49F4@illinois.edu> On Jul 20, 2010, at 12:53 PM, Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. > > So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. Not really abandoned, but it won't help in this case unless you intend on converting to BioSQL. > CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. Look at Bio::Schema:Chado. It's more middleware, no direct BioPerl bindings yet. > I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. > > Then there's the small matter of loading the hg18 annotations into the appropriate relational database. > > Thanks in advance for your guidance, > > Jonathan Bio::DB::SeqFeature::Store. Export the data into GTF; I think the database will load this (via Bio::DB::SeqFeature::Store::GFF2Loader). Otherwise, using the ensembl perl API is an option. One can install the database locally and use the Ensembl Perl API to extract the information you need. There were modules that were intended as interfaces to the remote UCSC databases but (IIRC) there was significant concern from the UCSC folks about overloading the UCSC server with queries, so they were basically deprecated (were only partially developed anyway). chris From hlapp at drycafe.net Tue Jul 20 15:40:10 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 20 Jul 2010 15:40:10 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <0369BC4D-9769-47AE-AF6C-B43BAAEC2327@drycafe.net> On Jul 20, 2010, at 1:53 PM, Jonathan Epstein wrote: > Biosql/BioPerl-db looks like the cleanest solution, but it's not > clear to me how up-to-date it is; it sort of looks like an abandoned > project. It's not abandoned at all. I'm not sure though it serves your use-case - it sounds like some GFF store would meet your needs much better. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From florent.angly at gmail.com Tue Jul 20 18:05:22 2010 From: florent.angly at gmail.com (Florent Angly) Date: Wed, 21 Jul 2010 08:05:22 +1000 Subject: [Bioperl-l] Fwd: gene extraction script Message-ID: <4C461DA2.5090009@gmail.com> -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ From awitney at sgul.ac.uk Wed Jul 21 04:02:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 09:02:01 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <84B8D550-E4CA-4027-99A8-D05F1B5E8DEE@sgul.ac.uk> Hi Nicholas, If you just want to retrieve sequences from GenBank, try this: http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl HTH adam On 20 Jul 2010, at 23:05, Florent Angly wrote: > > > -------- Original Message -------- > Subject: gene extraction script > Date: Tue, 20 Jul 2010 15:56:36 +0100 > From: Nicholas Brown > To: > > > > Hi, > > Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? > Thanks so much for your time in reading this. > > Kind Regards, > > Nicholas Brown > > Script > http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl > #!/usr/bin/perl -w > # $Id$ > =pod > > > =head1 NAME > > > extract_genes.pl - extract genomic sequences from NCBI files > using BioPerl > > > =head1 DESCRIPTION > > > This script is a simple solution to the problem of > extracting genomic regions corresponding to genes. There are other > solutions, this particular approach uses genomic sequence > files from NCBI and gene coordinates from Entrez Gene. > > > The first time this script is run it will be slow as it will > extract species-specific data from the gene2accession file and create > a storable hash (retrieving the positional data from this hash is > significantly faster than reading gene2accession each time the script > runs). The subsequent runs should be fast. > > > =head1 INSTALLATION > > > =head2 > > > Install BioPerl, full instructions at http://bioperl.org. > > > =head2 Download gene2accession.gz > > > Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into > your working directory and gunzip it. > > > =head2 Download sequence files > > > Create one or more species directories in the working directory, the > directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). > > > Download the nucleotide fasta files for a given species from its CHR* > directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a > species directory. The sequence files will have the suffix ".fna" or > "fa.gz", gunzip if necessary. > > > =head2 Determine Taxon id > > > Determine the taxon id for the given species. This id is the first column > in the gene2accession file. Modify the %species hash in this script > such that name of your species directory is a key and the taxon id is the > value. > > > =head2 Command-line options > > > -i Gene id > -s Name of species directory > -h Help > > > Example: > > > extract_genes.pl -i 850302 -s Sc > > > =cut > > > use strict; > use Bio::DB::Fasta; > use Getopt::Long; > use Storable; > > my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae > "Ec" => 83333, # Escherichia coli K12 > "Hs" => 9606 # H. sapiens > ); > > my ($help,$id,$name); > > GetOptions( "s=s" => \$name, > "i=i" => \$id, > "h" => \$help ); > > usage() if ($help || !$id || !$name); > > my $storedHash = $name . ".dump"; > > # create index for a directory of fasta files > my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); > > # extract species-specific data from gene2accession > unless (-e $storedHash) { > my $ref; > # extract species-specific information from gene2accession > open MYIN,"gene2accession" or die "No gene2accession file\n"; > while () { > my @arr = split "\t",$_; > if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { > ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, > $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = > ($arr[9], $arr[10], $arr[11], $arr[7]); > } > } > # save species-specific information using Storable > store $ref, $storedHash; > } > > # retrieve the species-specific data from a stored hash > my $ref = retrieve($storedHash); > > # retrieve sequence and sub-sequence > if (defined $ref->{$id}) { > my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); > my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); > $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); > > # Insert SeqIO options here... > print $seq->seq,"\n"; > } else { > print "Cannot find id: $id\n"; > } > > sub make_my_id { > my $line = shift; > $line =~ /ref\|([^|]+)/; > $1; > } > > sub usage { > system "perldoc $0"; > exit; > } > > __END__ > > > _______________________________________________ > 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 Jul 21 05:43:35 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 10:43:35 +0100 Subject: [Bioperl-l] Fwd: Fwd: gene extraction script References: <4C46B84C.4000702@univ-montp2.fr> Message-ID: forwarding to the original poster and the list... Begin forwarded message: > From: Laurent MANCHON > Date: 21 July 2010 10:05:16 GMT+01:00 > To: Adam Witney > Subject: Re: [Bioperl-l] Fwd: gene extraction script > Reply-To: lmanchon at univ-montp2.fr > > another program you can use. > > > #!/usr/bin/perl > # retrieve sequences from genbank > # read list of GenBank access number from a file and write to output.txt file > > use LWP::UserAgent; > use Bio::SeqIO; > use Bio::DB::GenBank; > $cpt=0; > $outfile = "outfile.txt"; > chomp($outfile); > $gb = new Bio::DB::GenBank; > while (<>) { > ($Fld1) = split(' ', $_, 9999); > $out = Bio::SeqIO->new('-file' => ">>$outfile",'-format' => 'fasta'); > $acc = $Fld1; > $cpt++; > print $acc,"\t$cpt"," retrieved\n"; > $seqio = $gb->get_Stream_by_acc([$acc]); > while( $seq = $seqio->next_seq() ) { > open(LOG,">>$outfile"); > printf LOG '%s ', ">" . $acc; > $out->write_seq($seq); > close(LOG); > } > > > > > > Adam Witney a ?crit : >> >> Hi Nicholas, >> >> If you just want to retrieve sequences from GenBank, try this: >> >> http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl >> >> HTH >> >> adam >> >> >> On 20 Jul 2010, at 23:05, Florent Angly wrote: >> >> >>> -------- Original Message -------- >>> Subject: gene extraction script >>> Date: Tue, 20 Jul 2010 15:56:36 +0100 >>> From: Nicholas Brown >>> To: >>> >>> >>> >>> Hi, >>> >>> Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? >>> Thanks so much for your time in reading this. >>> >>> Kind Regards, >>> >>> Nicholas Brown >>> >>> Script >>> http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl >>> #!/usr/bin/perl -w >>> # $Id$ >>> =pod >>> >>> >>> =head1 NAME >>> >>> >>> extract_genes.pl - extract genomic sequences from NCBI files >>> using BioPerl >>> >>> >>> =head1 DESCRIPTION >>> >>> >>> This script is a simple solution to the problem of >>> extracting genomic regions corresponding to genes. There are other >>> solutions, this particular approach uses genomic sequence >>> files from NCBI and gene coordinates from Entrez Gene. >>> >>> >>> The first time this script is run it will be slow as it will >>> extract species-specific data from the gene2accession file and create >>> a storable hash (retrieving the positional data from this hash is >>> significantly faster than reading gene2accession each time the script >>> runs). The subsequent runs should be fast. >>> >>> >>> =head1 INSTALLATION >>> >>> >>> =head2 >>> >>> >>> Install BioPerl, full instructions at http://bioperl.org. >>> >>> >>> =head2 Download gene2accession.gz >>> >>> >>> Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into >>> your working directory and gunzip it. >>> >>> >>> =head2 Download sequence files >>> >>> >>> Create one or more species directories in the working directory, the >>> directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). >>> >>> >>> Download the nucleotide fasta files for a given species from its CHR* >>> directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a >>> species directory. The sequence files will have the suffix ".fna" or >>> "fa.gz", gunzip if necessary. >>> >>> >>> =head2 Determine Taxon id >>> >>> >>> Determine the taxon id for the given species. This id is the first column >>> in the gene2accession file. Modify the %species hash in this script >>> such that name of your species directory is a key and the taxon id is the >>> value. >>> >>> >>> =head2 Command-line options >>> >>> >>> -i Gene id >>> -s Name of species directory >>> -h Help >>> >>> >>> Example: >>> >>> >>> extract_genes.pl -i 850302 -s Sc >>> >>> >>> =cut >>> >>> >>> use strict; >>> use Bio::DB::Fasta; >>> use Getopt::Long; >>> use Storable; >>> >>> my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae >>> "Ec" => 83333, # Escherichia coli K12 >>> "Hs" => 9606 # H. sapiens >>> ); >>> >>> my ($help,$id,$name); >>> >>> GetOptions( "s=s" => \$name, >>> "i=i" => \$id, >>> "h" => \$help ); >>> >>> usage() if ($help || !$id || !$name); >>> >>> my $storedHash = $name . ".dump"; >>> >>> # create index for a directory of fasta files >>> my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); >>> >>> # extract species-specific data from gene2accession >>> unless (-e $storedHash) { >>> my $ref; >>> # extract species-specific information from gene2accession >>> open MYIN,"gene2accession" or die "No gene2accession file\n"; >>> while () { >>> my @arr = split "\t",$_; >>> if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { >>> ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, >>> $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = >>> ($arr[9], $arr[10], $arr[11], $arr[7]); >>> } >>> } >>> # save species-specific information using Storable >>> store $ref, $storedHash; >>> } >>> >>> # retrieve the species-specific data from a stored hash >>> my $ref = retrieve($storedHash); >>> >>> # retrieve sequence and sub-sequence >>> if (defined $ref->{$id}) { >>> my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); >>> my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); >>> $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); >>> >>> # Insert SeqIO options here... >>> print $seq->seq,"\n"; >>> } else { >>> print "Cannot find id: $id\n"; >>> } >>> >>> sub make_my_id { >>> my $line = shift; >>> $line =~ /ref\|([^|]+)/; >>> $1; >>> } >>> >>> sub usage { >>> system "perldoc $0"; >>> exit; >>> } >>> >>> __END__ >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 jun.yin at ucd.ie Wed Jul 21 06:32:25 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Wed, 21 Jul 2010 11:32:25 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <012201cb28c0$027eb000$077c1000$%yin@ucd.ie> Hi, Nicolas, You don't need to edit the original code. Usually the package developed by the community provides enough methods for you. You may consider to use the recent developed package Bio::DB::EUtilities to retrieve the sequences from GenBank. See HOWTO here: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Florent Angly Sent: Tuesday, July 20, 2010 11:05 PM To: bioperl-l List; n.brown at nhm.ac.uk Subject: [Bioperl-l] Fwd: gene extraction script -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_ge nes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com From amritavisdom at gmail.com Sat Jul 17 07:21:27 2010 From: amritavisdom at gmail.com (AMRITA VISDOM) Date: Sat, 17 Jul 2010 16:51:27 +0530 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita From ycchen1981 at gmail.com Mon Jul 19 03:11:39 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Mon, 19 Jul 2010 15:11:39 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my ?$in ?= Bio::SeqIO->new(-file => "$inputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'abi'); my ?$out = Bio::SeqIO->new(-file => ">$outputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'phd'); while ( my $seq = $in->next_seq() ) { ? ? ? for my $curr(1 .. ?$seq->length()) { ? ? ? ? ? ? ? print "[",$seq->qualat($curr),"]:"; ? ? ? ? ? ? ? print "[",$seq->trace_index_at($curr),"]\t"; ? ? ? } ? ? ? $out->write_seq($seq); ? ? ? last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From amritavisdom at gmail.com Mon Jul 19 07:25:19 2010 From: amritavisdom at gmail.com (Amritavisdom) Date: Mon, 19 Jul 2010 04:25:19 -0700 (PDT) Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: <29203643.post@talk.nabble.com> Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita -- View this message in context: http://old.nabble.com/Parsing-Alternative-Splicing-Gene-information-from-Genbank-file-using-Bioperl-tp29203643p29203643.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From gabriel.jabud at gmail.com Tue Jul 20 14:36:54 2010 From: gabriel.jabud at gmail.com (Gabriel Ab) Date: Tue, 20 Jul 2010 11:36:54 -0700 (PDT) Subject: [Bioperl-l] Finding mutations in Blast files Message-ID: <29216321.post@talk.nabble.com> I'm trying to write a script to find mutations in a Blast output file. The result should look something like [A/G] (query/subject) for SNPs and [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if possible. I was able to get both the query and subject sequence extracted from blast files, but parsing through that for mutations without the help of modules and writing them like above is harder than it sounds. Deletions and other things in the alignment can make it very tricky. I tried looking for modules that would make this task easier but I couldn't find anything. Can someone point me in the right direction on how to do this or let me know about modules that could help? Thanks. -- View this message in context: http://old.nabble.com/Finding-mutations-in-Blast-files-tp29216321p29216321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From taw-bioperl at dowfamily.net Tue Jul 20 19:46:05 2010 From: taw-bioperl at dowfamily.net (Ycart) Date: Tue, 20 Jul 2010 23:46:05 +0000 (UTC) Subject: [Bioperl-l] Accessing karyotype data from Ensembl Message-ID: Hi, I am trying to figure out the correct syntax to access the karyotype data from the Ensembl database. I need to use the start and end base pair coordinates for the karyotype bands in a separate program, which means I need to be able to use that data, not just view it. I'm thinking that it will be like getting slices as described in the Core API Tutorial, but with some other word than 'Slice' in: my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); Any ideas on how to do this under the current API? -Tracy From cjfields at illinois.edu Wed Jul 21 17:43:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 16:43:32 -0500 Subject: [Bioperl-l] Accessing karyotype data from Ensembl In-Reply-To: References: Message-ID: You should contact the ensembl mail list for ensembl-related questions; this lies outside the bioperl domain. chris On Jul 20, 2010, at 6:46 PM, Ycart wrote: > Hi, > > I am trying to figure out the correct syntax to access the karyotype data from > the Ensembl database. I need to use the start and end base pair coordinates for > the karyotype bands in a separate program, which means I need to be able to use > that data, not just view it. > > I'm thinking that it will be like getting slices as described in the Core API > Tutorial, but with some other word than 'Slice' in: > my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); > > > Any ideas on how to do this under the current API? > > > -Tracy > > _______________________________________________ > 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 Jul 21 18:04:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 17:04:48 -0500 Subject: [Bioperl-l] Finding mutations in Blast files In-Reply-To: <29216321.post@talk.nabble.com> References: <29216321.post@talk.nabble.com> Message-ID: <1B5D46EC-BC67-43BB-9376-4A246CB093AD@illinois.edu> On Jul 20, 2010, at 1:36 PM, Gabriel Ab wrote: > > I'm trying to write a script to find mutations in a Blast output file. > The result should look something like [A/G] (query/subject) for SNPs and > [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if > possible. In order to get upstream and downstream you will need access to the original sequence (this information is not reported in the BLAST file). Use the HSP coords to pull that information. > I was able to get both the query and subject sequence extracted from blast > files, but parsing through that for mutations without the help of modules > and writing them like above is harder than it sounds. Deletions and other > things in the alignment can make it very tricky. I tried looking for > modules that would make this task easier but I couldn't find anything. ... > Can someone point me in the right direction on how to do this or let me know > about modules that could help? > > Thanks Bio::Search::HSP::GenericHSP::seq_inds() does something along these lines, e.g. iterates through the two strings by index position and stores relevant information. In this case, you would just print out [X/Y] where there is no match, or [--/XY] when gaps are present. Look at the code for that method to get the general idea. chris From David.Messina at sbc.su.se Wed Jul 21 18:43:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 21 Jul 2010 16:43:07 -0600 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl In-Reply-To: <29203643.post@talk.nabble.com> References: <29203643.post@talk.nabble.com> Message-ID: Hi Amrita, You will want to read the Feature Annotation HOWTO for details of how to parse a Genbank file: http://www.bioperl.org/wiki/HOWTO:Feature-Annotation Dave From cjfields at illinois.edu Wed Jul 21 20:09:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 19:09:05 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: Message-ID: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> It's very possible this is due to API changes within io_lib, but I can't be sure. Aaron, any idea? Just to note, we no longer recommend using the bioperl-ext modules, mainly b/c they have not been actively maintained, so much so that updating them to use the current API is quite difficult (might involve some extensive refactoring). The BioLib project, however, has perl bindings to io_lib. If one had time they could incorporate the BioLib io_lib bindings into bioperl, but I believe ABI support was removed a while ago so that will be problematic. chris On Jul 19, 2010, at 2:11 AM, ??? wrote: > Hi, > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > bioperl-ext-1.5.1, and io-lib-1.8.11; > my OS was 32-bit, Centos 5.2. > When I convert abi-format files to phd-format files, > the value of quality of all bases are '0', and the value of > trace_index of all bases are undefined. > Is there any possible reason leading to this problem? > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > 0.980904.e in phd files; > if this is the case, where can I find phred executers? > > The following is the code utilizing BioPerl and results from BioPerl > and Phred respectively: > ============================================== > #!/usr/bin/perl -w > unshift(@INC, "/opt/BioPerl-1.6.1/"); > unshift(@INC, "/opt/bioperl-ext"); > use strict; > use Bio::SeqIO; > > my $inputfilename='./HMA040184H12.T3.ab1'; > my $outputfilename='test11.phd'; > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > -format => 'abi'); > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > -format => 'phd'); > > while ( my $seq = $in->next_seq() ) { > for my $curr(1 .. $seq->length()) { > print "[",$seq->qualat($curr),"]:"; > print "[",$seq->trace_index_at($curr),"]\t"; > } > $out->write_seq($seq); > last; > } > > ================== test11.phd (by Bio::SeqIO) ================= > BEGIN_SEQUENCE (null) > > BEGIN_COMMENT > > CHROMAT_FILE: unknown > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.980904.e > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Mon Jul 19 11:59:09 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: unknown > CHEM: unknown > DYE: unknown > > END_COMMENT > > BEGIN_DNA > A 0 > G 0 > G 0 > G 0 > G 0 > . > . > . > . > > G 0 > T 0 > T 0 > G 0 > T 0 > C 0 > G 0 > C 0 > T 0 > A 0 > C 0 > END_DNA > > END_SEQUENCE > > ================== .phd (by phred 0.020425.c) ======================= > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > BEGIN_COMMENT > > CHROMAT_FILE: HMA040184H12.T3.ab1 > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.020425.c > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Fri Jul 9 16:20:59 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: 11905 > TRIM: 38 900 0.0500 > TRACE_PEAK_AREA_RATIO: 0.0630 > CHEM: term > DYE: big > > END_COMMENT > > BEGIN_DNA > a 11 2 > g 11 13 > g 11 22 > a 11 37 > a 11 52 > g 8 65 > c 6 76 > t 6 91 > c 6 97 > . > . > . > a 14 11840 > c 16 11849 > a 16 11861 > a 12 11873 > c 12 11885 > g 12 11897 > END_DNA > > END_SEQUENCE > ================================================ > Sincerely yours, > Yen-Chang Chen > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From amackey at virginia.edu Wed Jul 21 20:36:02 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Wed, 21 Jul 2010 20:36:02 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the bioperl-ext modules are not installed? Regardless, can you get a dump of the $seq objects before you hand them off to Bio::SeqIO::phd -- have the qual scores already been lost (problem with the abi reader), or not (problem with the phd writer)? And a basic question -- I assume your .abi files actually have quality values in them (not all do)? -Aaron On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > It's very possible this is due to API changes within io_lib, but I can't be > sure. Aaron, any idea? > > Just to note, we no longer recommend using the bioperl-ext modules, mainly > b/c they have not been actively maintained, so much so that updating them to > use the current API is quite difficult (might involve some extensive > refactoring). The BioLib project, however, has perl bindings to io_lib. If > one had time they could incorporate the BioLib io_lib bindings into bioperl, > but I believe ABI support was removed a while ago so that will be > problematic. > > chris > > On Jul 19, 2010, at 2:11 AM, ??? wrote: > > > Hi, > > > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > > bioperl-ext-1.5.1, and io-lib-1.8.11; > > my OS was 32-bit, Centos 5.2. > > When I convert abi-format files to phd-format files, > > the value of quality of all bases are '0', and the value of > > trace_index of all bases are undefined. > > Is there any possible reason leading to this problem? > > > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > > 0.980904.e in phd files; > > if this is the case, where can I find phred executers? > > > > The following is the code utilizing BioPerl and results from BioPerl > > and Phred respectively: > > ============================================== > > #!/usr/bin/perl -w > > unshift(@INC, "/opt/BioPerl-1.6.1/"); > > unshift(@INC, "/opt/bioperl-ext"); > > use strict; > > use Bio::SeqIO; > > > > my $inputfilename='./HMA040184H12.T3.ab1'; > > my $outputfilename='test11.phd'; > > > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > > -format => 'abi'); > > > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > > -format => 'phd'); > > > > while ( my $seq = $in->next_seq() ) { > > for my $curr(1 .. $seq->length()) { > > print "[",$seq->qualat($curr),"]:"; > > print "[",$seq->trace_index_at($curr),"]\t"; > > } > > $out->write_seq($seq); > > last; > > } > > > > ================== test11.phd (by Bio::SeqIO) ================= > > BEGIN_SEQUENCE (null) > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: unknown > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.980904.e > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Mon Jul 19 11:59:09 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: unknown > > CHEM: unknown > > DYE: unknown > > > > END_COMMENT > > > > BEGIN_DNA > > A 0 > > G 0 > > G 0 > > G 0 > > G 0 > > . > > . > > . > > . > > > > G 0 > > T 0 > > T 0 > > G 0 > > T 0 > > C 0 > > G 0 > > C 0 > > T 0 > > A 0 > > C 0 > > END_DNA > > > > END_SEQUENCE > > > > ================== .phd (by phred 0.020425.c) ======================= > > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: HMA040184H12.T3.ab1 > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.020425.c > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Fri Jul 9 16:20:59 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: 11905 > > TRIM: 38 900 0.0500 > > TRACE_PEAK_AREA_RATIO: 0.0630 > > CHEM: term > > DYE: big > > > > END_COMMENT > > > > BEGIN_DNA > > a 11 2 > > g 11 13 > > g 11 22 > > a 11 37 > > a 11 52 > > g 8 65 > > c 6 76 > > t 6 91 > > c 6 97 > > . > > . > > . > > a 14 11840 > > c 16 11849 > > a 16 11861 > > a 12 11873 > > c 12 11885 > > g 12 11897 > > END_DNA > > > > END_SEQUENCE > > ================================================ > > Sincerely yours, > > Yen-Chang Chen > > > > _______________________________________________ > > 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 Jul 21 22:41:16 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 21:41:16 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Nope; doesn't appear to be a pure-perl parser for this. Was there one? chris On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > bioperl-ext modules are not installed? > > Regardless, can you get a dump of the $seq objects before you hand them off > to Bio::SeqIO::phd -- have the qual scores already been lost (problem with > the abi reader), or not (problem with the phd writer)? > > And a basic question -- I assume your .abi files actually have quality > values in them (not all do)? > > -Aaron > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > >> It's very possible this is due to API changes within io_lib, but I can't be >> sure. Aaron, any idea? >> >> Just to note, we no longer recommend using the bioperl-ext modules, mainly >> b/c they have not been actively maintained, so much so that updating them to >> use the current API is quite difficult (might involve some extensive >> refactoring). The BioLib project, however, has perl bindings to io_lib. If >> one had time they could incorporate the BioLib io_lib bindings into bioperl, >> but I believe ABI support was removed a while ago so that will be >> problematic. >> >> chris >> >> On Jul 19, 2010, at 2:11 AM, ??? wrote: >> >>> Hi, >>> >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, >>> bioperl-ext-1.5.1, and io-lib-1.8.11; >>> my OS was 32-bit, Centos 5.2. >>> When I convert abi-format files to phd-format files, >>> the value of quality of all bases are '0', and the value of >>> trace_index of all bases are undefined. >>> Is there any possible reason leading to this problem? >>> >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is >>> 0.980904.e in phd files; >>> if this is the case, where can I find phred executers? >>> >>> The following is the code utilizing BioPerl and results from BioPerl >>> and Phred respectively: >>> ============================================== >>> #!/usr/bin/perl -w >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); >>> unshift(@INC, "/opt/bioperl-ext"); >>> use strict; >>> use Bio::SeqIO; >>> >>> my $inputfilename='./HMA040184H12.T3.ab1'; >>> my $outputfilename='test11.phd'; >>> >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", >>> -format => 'abi'); >>> >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", >>> -format => 'phd'); >>> >>> while ( my $seq = $in->next_seq() ) { >>> for my $curr(1 .. $seq->length()) { >>> print "[",$seq->qualat($curr),"]:"; >>> print "[",$seq->trace_index_at($curr),"]\t"; >>> } >>> $out->write_seq($seq); >>> last; >>> } >>> >>> ================== test11.phd (by Bio::SeqIO) ================= >>> BEGIN_SEQUENCE (null) >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: unknown >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.980904.e >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Mon Jul 19 11:59:09 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: unknown >>> CHEM: unknown >>> DYE: unknown >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> A 0 >>> G 0 >>> G 0 >>> G 0 >>> G 0 >>> . >>> . >>> . >>> . >>> >>> G 0 >>> T 0 >>> T 0 >>> G 0 >>> T 0 >>> C 0 >>> G 0 >>> C 0 >>> T 0 >>> A 0 >>> C 0 >>> END_DNA >>> >>> END_SEQUENCE >>> >>> ================== .phd (by phred 0.020425.c) ======================= >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: HMA040184H12.T3.ab1 >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.020425.c >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Fri Jul 9 16:20:59 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: 11905 >>> TRIM: 38 900 0.0500 >>> TRACE_PEAK_AREA_RATIO: 0.0630 >>> CHEM: term >>> DYE: big >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> a 11 2 >>> g 11 13 >>> g 11 22 >>> a 11 37 >>> a 11 52 >>> g 8 65 >>> c 6 76 >>> t 6 91 >>> c 6 97 >>> . >>> . >>> . >>> a 14 11840 >>> c 16 11849 >>> a 16 11861 >>> a 12 11873 >>> c 12 11885 >>> g 12 11897 >>> END_DNA >>> >>> END_SEQUENCE >>> ================================================ >>> Sincerely yours, >>> Yen-Chang Chen >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 alperyilmaz at gmail.com Thu Jul 22 00:09:38 2010 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Thu, 22 Jul 2010 00:09:38 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO Message-ID: Hi, I was using Bio::SeqIO with perl one-liner and I noticed an oddity. Can someone suggest a correction or workaround? Let test.fa be; >1 AGTC >2 CTGA Then, commandline below prints the expected output: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < test.fa output: 1 AGTC 2 CTGA However, if use the command in a pipe, then the output has an issue with primary_id of initial sequence. $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' output: AGTC 2 CTGA What is the workaround to make Bio::SeqIO work correctly in a one-liner with pipes? thanks, Alper Yilmaz Post-doctoral Researcher Plant Biotechnology Center The Ohio State University 1060 Carmack Rd Columbus, OH 43210 (614)688-4954 PS: Normally, the example is demonstrating useless use of cat, for the sake giving an example, it can be "command1 | command2 | command3 | perl -MBioSeqIO -e'...' " instead.. From fs5 at sanger.ac.uk Thu Jul 22 06:48:25 2010 From: fs5 at sanger.ac.uk (Frank Schwach) Date: Thu, 22 Jul 2010 11:48:25 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: Message-ID: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Hi Alper, You can actually reproduce it also by providing STDIN from keyboard input like so: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >1 aaaaaaaaa >2 aaaaaaaaa ggggggggg >3 2 ggggggggg ccccccccc 3 ccccccccc In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} then the command returned the sequence of the first entry without the ID again. >From the second entry onwards, it is all correct. I'm not 100% sure but could it be linked to buffering? SeqIO has to read ahead to find a complete entry that spans multiple lines. When you get STDIN from a file, you will get buffering and receive more than one line at once, which will allow the next_seq method to work as expected. If you provide line-by-line input then that method probably can't work correctly. If that is the case then you can't use the command in a pipe at all. Frank On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: > Hi, > > I was using Bio::SeqIO with perl one-liner and I noticed an oddity. > Can someone suggest a correction or workaround? > > Let test.fa be; > >1 > AGTC > >2 > CTGA > > Then, commandline below prints the expected output: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < > test.fa > > output: > 1 AGTC > 2 CTGA > > However, if use the command in a pipe, then the output has an issue > with primary_id of initial sequence. > $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > =>\*STDIN); while ($myseq=$seq->next_seq){ print > $myseq->id,"\t",$myseq->seq,"\n"}' > > output: > AGTC > 2 CTGA > > What is the workaround to make Bio::SeqIO work correctly in a > one-liner with pipes? > > thanks, > > Alper Yilmaz > Post-doctoral Researcher > Plant Biotechnology Center > The Ohio State University > 1060 Carmack Rd > Columbus, OH 43210 > (614)688-4954 > > > PS: Normally, the example is demonstrating useless use of cat, for the > sake giving an example, it can be "command1 | command2 | command3 | > perl -MBioSeqIO -e'...' " instead.. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- 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 roy.chaudhuri at gmail.com Thu Jul 22 07:49:41 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 12:49:41 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Message-ID: <4C483055.5050402@gmail.com> Hi Alper, The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. Cheers. Roy. On 22/07/2010 11:48, Frank Schwach wrote: > Hi Alper, > > You can actually reproduce it also by providing STDIN from keyboard > input like so: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >> 1 > aaaaaaaaa >> 2 > aaaaaaaaa > ggggggggg >> 3 > 2 ggggggggg > ccccccccc > 3 ccccccccc > > In this case I typed > ">1"[ENTER] > "aaaaaaaaa"[ENTER] > ">2"[ENTER} > then the command returned the sequence of the first entry without the ID > again. >> From the second entry onwards, it is all correct. > > I'm not 100% sure but could it be linked to buffering? SeqIO has to read > ahead to find a complete entry that spans multiple lines. When you get > STDIN from a file, you will get buffering and receive more than one line > at once, which will allow the next_seq method to work as expected. If > you provide line-by-line input then that method probably can't work > correctly. > If that is the case then you can't use the command in a pipe at all. > > Frank > > > > On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >> Hi, >> >> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >> Can someone suggest a correction or workaround? >> >> Let test.fa be; >>> 1 >> AGTC >>> 2 >> CTGA >> >> Then, commandline below prints the expected output: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >> test.fa >> >> output: >> 1 AGTC >> 2 CTGA >> >> However, if use the command in a pipe, then the output has an issue >> with primary_id of initial sequence. >> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> $myseq->id,"\t",$myseq->seq,"\n"}' >> >> output: >> AGTC >> 2 CTGA >> >> What is the workaround to make Bio::SeqIO work correctly in a >> one-liner with pipes? >> >> thanks, >> >> Alper Yilmaz >> Post-doctoral Researcher >> Plant Biotechnology Center >> The Ohio State University >> 1060 Carmack Rd >> Columbus, OH 43210 >> (614)688-4954 >> >> >> PS: Normally, the example is demonstrating useless use of cat, for the >> sake giving an example, it can be "command1 | command2 | command3 | >> perl -MBioSeqIO -e'...' " instead.. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From amackey at virginia.edu Thu Jul 22 09:19:52 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 09:19:52 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Message-ID: Hmm, perhaps I'm thinking about the SCF code, not the ABI code. -Aaron On Wed, Jul 21, 2010 at 10:41 PM, Chris Fields wrote: > Nope; doesn't appear to be a pure-perl parser for this. Was there one? > > chris > > On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > > > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > > bioperl-ext modules are not installed? > > > > Regardless, can you get a dump of the $seq objects before you hand them > off > > to Bio::SeqIO::phd -- have the qual scores already been lost (problem > with > > the abi reader), or not (problem with the phd writer)? > > > > And a basic question -- I assume your .abi files actually have quality > > values in them (not all do)? > > > > -Aaron > > > > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields > wrote: > > > >> It's very possible this is due to API changes within io_lib, but I can't > be > >> sure. Aaron, any idea? > >> > >> Just to note, we no longer recommend using the bioperl-ext modules, > mainly > >> b/c they have not been actively maintained, so much so that updating > them to > >> use the current API is quite difficult (might involve some extensive > >> refactoring). The BioLib project, however, has perl bindings to io_lib. > If > >> one had time they could incorporate the BioLib io_lib bindings into > bioperl, > >> but I believe ABI support was removed a while ago so that will be > >> problematic. > >> > >> chris > >> > >> On Jul 19, 2010, at 2:11 AM, ??? wrote: > >> > >>> Hi, > >>> > >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > >>> bioperl-ext-1.5.1, and io-lib-1.8.11; > >>> my OS was 32-bit, Centos 5.2. > >>> When I convert abi-format files to phd-format files, > >>> the value of quality of all bases are '0', and the value of > >>> trace_index of all bases are undefined. > >>> Is there any possible reason leading to this problem? > >>> > >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > >>> 0.980904.e in phd files; > >>> if this is the case, where can I find phred executers? > >>> > >>> The following is the code utilizing BioPerl and results from BioPerl > >>> and Phred respectively: > >>> ============================================== > >>> #!/usr/bin/perl -w > >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); > >>> unshift(@INC, "/opt/bioperl-ext"); > >>> use strict; > >>> use Bio::SeqIO; > >>> > >>> my $inputfilename='./HMA040184H12.T3.ab1'; > >>> my $outputfilename='test11.phd'; > >>> > >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", > >>> -format => 'abi'); > >>> > >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", > >>> -format => 'phd'); > >>> > >>> while ( my $seq = $in->next_seq() ) { > >>> for my $curr(1 .. $seq->length()) { > >>> print "[",$seq->qualat($curr),"]:"; > >>> print "[",$seq->trace_index_at($curr),"]\t"; > >>> } > >>> $out->write_seq($seq); > >>> last; > >>> } > >>> > >>> ================== test11.phd (by Bio::SeqIO) ================= > >>> BEGIN_SEQUENCE (null) > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: unknown > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.980904.e > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Mon Jul 19 11:59:09 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: unknown > >>> CHEM: unknown > >>> DYE: unknown > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> A 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> . > >>> . > >>> . > >>> . > >>> > >>> G 0 > >>> T 0 > >>> T 0 > >>> G 0 > >>> T 0 > >>> C 0 > >>> G 0 > >>> C 0 > >>> T 0 > >>> A 0 > >>> C 0 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> > >>> ================== .phd (by phred 0.020425.c) ======================= > >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: HMA040184H12.T3.ab1 > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.020425.c > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Fri Jul 9 16:20:59 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: 11905 > >>> TRIM: 38 900 0.0500 > >>> TRACE_PEAK_AREA_RATIO: 0.0630 > >>> CHEM: term > >>> DYE: big > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> a 11 2 > >>> g 11 13 > >>> g 11 22 > >>> a 11 37 > >>> a 11 52 > >>> g 8 65 > >>> c 6 76 > >>> t 6 91 > >>> c 6 97 > >>> . > >>> . > >>> . > >>> a 14 11840 > >>> c 16 11849 > >>> a 16 11861 > >>> a 12 11873 > >>> c 12 11885 > >>> g 12 11897 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> ================================================ > >>> Sincerely yours, > >>> Yen-Chang Chen > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/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 Jul 22 09:27:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 08:27:30 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C483055.5050402@gmail.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> Message-ID: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Would someone like to file this as a bug? My guess is this may be a combination of using pipes and the way FASTA is parsed (locally resets $/). http://bugzilla.open-bio.org chris On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > Hi Alper, > > The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. > > Cheers. > Roy. > > On 22/07/2010 11:48, Frank Schwach wrote: >> Hi Alper, >> >> You can actually reproduce it also by providing STDIN from keyboard >> input like so: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >>> 1 >> aaaaaaaaa >>> 2 >> aaaaaaaaa >> ggggggggg >>> 3 >> 2 ggggggggg >> ccccccccc >> 3 ccccccccc >> >> In this case I typed >> ">1"[ENTER] >> "aaaaaaaaa"[ENTER] >> ">2"[ENTER} >> then the command returned the sequence of the first entry without the ID >> again. >>> From the second entry onwards, it is all correct. >> >> I'm not 100% sure but could it be linked to buffering? SeqIO has to read >> ahead to find a complete entry that spans multiple lines. When you get >> STDIN from a file, you will get buffering and receive more than one line >> at once, which will allow the next_seq method to work as expected. If >> you provide line-by-line input then that method probably can't work >> correctly. >> If that is the case then you can't use the command in a pipe at all. >> >> Frank >> >> >> >> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>> Hi, >>> >>> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >>> Can someone suggest a correction or workaround? >>> >>> Let test.fa be; >>>> 1 >>> AGTC >>>> 2 >>> CTGA >>> >>> Then, commandline below prints the expected output: >>> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >>> test.fa >>> >>> output: >>> 1 AGTC >>> 2 CTGA >>> >>> However, if use the command in a pipe, then the output has an issue >>> with primary_id of initial sequence. >>> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>> >>> output: >>> AGTC >>> 2 CTGA >>> >>> What is the workaround to make Bio::SeqIO work correctly in a >>> one-liner with pipes? >>> >>> thanks, >>> >>> Alper Yilmaz >>> Post-doctoral Researcher >>> Plant Biotechnology Center >>> The Ohio State University >>> 1060 Carmack Rd >>> Columbus, OH 43210 >>> (614)688-4954 >>> >>> >>> PS: Normally, the example is demonstrating useless use of cat, for the >>> sake giving an example, it can be "command1 | command2 | command3 | >>> perl -MBioSeqIO -e'...' " instead.. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 roy.chaudhuri at gmail.com Thu Jul 22 09:41:00 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 14:41:00 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C484A6C.1000502@gmail.com> Done (bug 3122). On 22/07/2010 14:27, Chris Fields wrote: > Would someone like to file this as a bug? My guess is this may be a > combination of using pipes and the way FASTA is parsed (locally > resets $/). > > http://bugzilla.open-bio.org > > chris > > On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > >> Hi Alper, >> >> The problem comes about because you don't specify -format=>'fasta' >> in your Bio::SeqIO object. BioPerl attempts to guess the format if >> you don't specify it, but seems to be struggling in this case. I >> can't really think of any good reason for not specifying the >> format. Just in case anyone wants to investigate further, I noticed >> that if you try the example with longer fasta sequences, the first >> line of the sequence is interpreted as the id, with the remainder >> as the sequence. >> >> Cheers. Roy. >> >> On 22/07/2010 11:48, Frank Schwach wrote: >>> Hi Alper, >>> >>> You can actually reproduce it also by providing STDIN from >>> keyboard input like so: $ perl -MBio::SeqIO -e 'my >>> $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> 1 >>> aaaaaaaaa >>>> 2 >>> aaaaaaaaa ggggggggg >>>> 3 >>> 2 ggggggggg ccccccccc 3 ccccccccc >>> >>> In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} >>> then the command returned the sequence of the first entry without >>> the ID again. >>>> From the second entry onwards, it is all correct. >>> >>> I'm not 100% sure but could it be linked to buffering? SeqIO has >>> to read ahead to find a complete entry that spans multiple lines. >>> When you get STDIN from a file, you will get buffering and >>> receive more than one line at once, which will allow the next_seq >>> method to work as expected. If you provide line-by-line input >>> then that method probably can't work correctly. If that is the >>> case then you can't use the command in a pipe at all. >>> >>> Frank >>> >>> >>> >>> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>>> Hi, >>>> >>>> I was using Bio::SeqIO with perl one-liner and I noticed an >>>> oddity. Can someone suggest a correction or workaround? >>>> >>>> Let test.fa be; >>>>> 1 >>>> AGTC >>>>> 2 >>>> CTGA >>>> >>>> Then, commandline below prints the expected output: $ perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}'< test.fa >>>> >>>> output: 1 AGTC 2 CTGA >>>> >>>> However, if use the command in a pipe, then the output has an >>>> issue with primary_id of initial sequence. $ cat test.fa | perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> >>>> output: AGTC 2 CTGA >>>> >>>> What is the workaround to make Bio::SeqIO work correctly in a >>>> one-liner with pipes? >>>> >>>> thanks, >>>> >>>> Alper Yilmaz Post-doctoral Researcher Plant Biotechnology >>>> Center The Ohio State University 1060 Carmack Rd Columbus, OH >>>> 43210 (614)688-4954 >>>> >>>> >>>> PS: Normally, the example is demonstrating useless use of cat, >>>> for the sake giving an example, it can be "command1 | command2 >>>> | command3 | perl -MBioSeqIO -e'...' " instead.. >>>> _______________________________________________ Bioperl-l >>>> mailing list Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 sheetu.piscean at gmail.com Wed Jul 21 17:49:25 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Wed, 21 Jul 2010 14:49:25 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Adding some more details on OS and BioPerl version OS: sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 UTC 2010 i686 GNU/Linux Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi BioPerl Version : sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' 1.006001 Attached is the error that I get while running the RemoteBlast. Thanks, Sheetal On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani wrote: > Hi, > > I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > is the complete script : > #Remote-blast "factory object" creation and blast-parameter > initialization > > use Bio::Tools::Run::RemoteBlast; > use strict; > my $prog = 'blastx'; > my $db = 'nr/nt'; > my $e_val= '1e-10'; > > my @params = ( '-prog' => $prog, > '-data' => $db, > '-expect' => $e_val, > '-readmethod' => 'SearchIO' ); > > my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > #$v is just to turn on and off the messages > my $v = 0; > > my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > ); > > while (my $input = $str->next_seq()){ > #Blast a sequence against a database: > > #Alternatively, you could pass in a file with many > #sequences rather than loop through sequence one at a time > #Remove the loop starting 'while (my $input = $str->next_seq())' > #and swap the two lines below for an example of that. > my $r = $factory->submit_blast($input); > #my $r = $factory->submit_blast('amino.fa'); > > print STDERR "waiting..." if( $v > 0 ); > while ( my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = $factory->retrieve_blast($rid); > if( !ref($rc) ) { > if( $rc < 0 ) { > print "removing rid as rc is < 0"; > $factory->remove_rid($rid); > } > print STDERR "." if ( $v > 0 ); > sleep 5; > } else { > my $result = $rc->next_result(); > #save the output > print "saving to file"; > my $filename = "contig_236.out"; #$result->query_name()."\.out"; > $factory->save_output($filename); > $factory->remove_rid($rid); > print "\nQuery Name: ", $result->query_name(), "\n"; > while ( my $hit = $result->next_hit ) { > next unless ( $v > 0); > print "\thit name is ", $hit->name, "\n"; > while( my $hsp = $hit->next_hsp ) { > print "\t\tscore is ", $hsp->score, "\n"; > } > } > } > } > } > } > > But when I run this, I get an error in html format which says "Cannot > accept request, error code: -103". Attaching the error file for reference. > Can you please help me with debugging this error? Your help is much > appreciated. > > Also, informing about the previous error that I fixed by adding this line: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > I was getting prior to adding this line was : > --------------------- WARNING --------------------- > MSG:

An error has occurred on the > server, The server is unable to format right now, please try again in a few > minutes. If the problem (Informational Message: No alias or index file > found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4CF5MY9101P

> > It kinda took me a while to find out the 2 requirements > > # 1) set your database like this: > -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > > # 2) add this line before submitting the job: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > I think it will be great if you can add this to the synopsis section of > RemoteBlast.pm > > Thanks, > Sheetal > -------------- next part -------------- An HTML attachment was scrubbed... URL: From evelyne.c88 at gmail.com Thu Jul 22 09:57:47 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 06:57:47 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> Message-ID: <29237193.post@talk.nabble.com> Hi, I would like to run a SW alignment, but i'm new to programming... Tried using several tutorials to install this Bioperl-ext package, but not getting that far... Maybe you can help? -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29237193.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From biopython at maubp.freeserve.co.uk Thu Jul 22 10:41:21 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 15:41:21 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29237193.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: > > Hi, > > I would like to run a SW alignment, but i'm new to programming... > Tried using several tutorials to install this Bioperl-ext package, but not > getting that far... > Maybe you can help? How about using the water tool in EMBOSS? I'm sure BioPerl has wrappers for that... http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html Peter From cjfields at illinois.edu Thu Jul 22 11:31:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 10:31:30 -0500 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Jul 22, 2010, at 9:41 AM, Peter wrote: > On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: >> >> Hi, >> >> I would like to run a SW alignment, but i'm new to programming... >> Tried using several tutorials to install this Bioperl-ext package, but not >> getting that far... >> Maybe you can help? > > How about using the water tool in EMBOSS? I'm sure BioPerl has > wrappers for that... > > http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html > > Peter Yes, we do. I would suggest that solution as well; the SW work in bioperl-ext hasn't been maintained actively for a while. That doesn't mean it won't suit your needs, but issues with compilation will likely remained unaddressed. chris From evelyne.c88 at gmail.com Thu Jul 22 10:09:30 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 07:09:30 -0700 (PDT) Subject: [Bioperl-l] installing Bioperl-ext package (Bio::Tools::pSW) Message-ID: <29237314.post@talk.nabble.com> Hi I'm kind of a rookie at programming, but i'm trying to align two sequences. And i would like to use Bio::Tools::pSW I have followed instructions and installed a C compiler (devC++) I read a lot of different tutorials, but cannot find a way to install this package, everything i try gives errors latest error when i tried 'install B/BIRNEY/bioperl-ext-1.4.tar.gz' : c:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site' returned status 512, won't make running make test make had some problems, won't test running make install make had some problems, won't install -- View this message in context: http://old.nabble.com/installing-Bioperl-ext-package-%28Bio%3A%3ATools%3A%3ApSW%29-tp29237314p29237314.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From evelyne.c88 at gmail.com Thu Jul 22 11:21:17 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:21:17 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: <29238161.post@talk.nabble.com> I have really no idea what that means... Studying first year of bio-informatics, and have to make a small perl program as exam Maybe I'm in a bit over my head, I'll ask the tutor for some advice... < References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C4855EE.1010208@bms.com> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm if (defined $self->{-file}) { # Close the file we opened. close($fh); } elsif (ref $fh eq 'GLOB') { # Try seeking to the start position. >>> seek($fh, $start_pos, 0); } elsif (defined $fh && $fh->can('setpos')) { # Seek to the start position. $fh->setpos($start_pos); } return ($done ? $fmt_string : undef); seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset is where the second non-null line starts. I am not sure why- all manuals claim this should work? Hope this helps. Stefan On 7/22/2010 9:27 AM, Chris Fields wrote: > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From biopython at maubp.freeserve.co.uk Thu Jul 22 11:42:25 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 16:42:25 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29238161.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: > > I have really no idea what that means... > Studying first year of bio-informatics, and have to make a small perl > program as exam > Maybe I'm in a bit over my head, I'll ask the tutor for some advice... > The EMBOSS project is a collection of open source command line tools written in C, and includes a tool called "water" for doing Smith Waterman (SW) sequence alignments. I was suggesting you could use BioPerl to call this needle program and parse its output. However, it sounds like you actually have a programming assignment where the point is to actually implement the SW algorithm yourself (in perl). In this case, EMBOSS won't be useful after all. Peter From evelyne.c88 at gmail.com Thu Jul 22 11:53:39 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:53:39 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: <29238557.post@talk.nabble.com> There is actually no real assignment with a goal described. We only have to prove that we understand and can use Perl. (Description of the course states we are to learn the concepts of computer programming, and rudimentary Perl) The Smith Waterman Tool was mentioned during the courses (along with BPlite, and using remote and local BLASTs) so i wanted to explore this, without really knowing how complicated the use of this could be... Maybe they just wanted to let us know what possibilities there are, without expecting that we could do this on our own... Peter-329 wrote: > > On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: >> >> I have really no idea what that means... >> Studying first year of bio-informatics, and have to make a small perl >> program as exam >> Maybe I'm in a bit over my head, I'll ask the tutor for some advice... >> > > The EMBOSS project is a collection of open source command line > tools written in C, and includes a tool called "water" for doing Smith > Waterman (SW) sequence alignments. I was suggesting you could > use BioPerl to call this needle program and parse its output. > > However, it sounds like you actually have a programming assignment > where the point is to actually implement the SW algorithm yourself (in > perl). In this case, EMBOSS won't be useful after all. > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29238557.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From amackey at virginia.edu Thu Jul 22 13:15:18 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 13:15:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C4855EE.1010208@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. -Aaron On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov wrote: > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset > is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> > > > _______________________________________________ > 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 Jul 22 14:35:51 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 13:35:51 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C48853F.3050904@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): tell() on pipes, fifos, and sockets usually returns -1. My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: if (!$self->seekable) { #die a horrible death } chris On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). > I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) > I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. > Another option is to right to a temp file or slurp into memory. This could be dangerous though... > > On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >> >> -Aaron >> >> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: >> >> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >> >> if (defined $self->{-file}) { >> # Close the file we opened. >> close($fh); >> } elsif (ref $fh eq 'GLOB') { >> # Try seeking to the start position. >> >>> seek($fh, $start_pos, 0); >> } elsif (defined $fh && $fh->can('setpos')) { >> # Seek to the start position. >> $fh->setpos($start_pos); >> } >> return ($done ? $fmt_string : undef); >> >> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >> after reset is where the second non-null line starts. >> I am not sure why- all manuals claim this should work? >> Hope this helps. >> Stefan >> >> On 7/22/2010 9:27 AM, Chris Fields wrote: >> >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > From dunlopjp.ctr at afrl.hpc.mil Thu Jul 22 12:35:01 2010 From: dunlopjp.ctr at afrl.hpc.mil (Mr. James P. Dunlop (Contractor)) Date: Thu, 22 Jul 2010 12:35:01 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org Message-ID: <4C487335.4080808@afrl.hpc.mil> Hello I very new to this type of install. I am trying to install this as non root, which may be part of the problem, but I thought I found some information that addresses this. Also I'm trying to use cpan. The error before termination is: Files=44, Tests=1140, 30 wallclock secs (22.97 cusr + 6.94 csys = 29.91 CPU) /usr/bin/make test -- OK Running make install /usr/bin/perl Build --makefile_env_macros 1 install Building Module-Build Writing /app/bioperl/BioPerl-1.6.0/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Module/Build/.packlist /usr/bin/make install -- OK Couldn't install Module::Build, giving up. Running make test Make had some problems, maybe interrupted? Won't test Running make install Make had some problems, maybe interrupted? Won't install cpan> Is there anything that is obvious to you folks? Would it be possible to cc any e-mails to dunlopjp at aol.com? Thanks Jim Dunlop 937-255-0050 From stefan.kirov at bms.com Thu Jul 22 13:51:59 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 13:51:59 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: <4C48853F.3050904@bms.com> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. Another option is to right to a temp file or slurp into memory. This could be dangerous though... On 7/22/2010 1:15 PM, Aaron Mackey wrote: > You cannot seek on a pipe, unfortunately. SeqIO should probably try > to detect this, and die rather than invoking GuessSeqFormat. > > -Aaron > > On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: > > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh > after reset is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From stefan.kirov at bms.com Thu Jul 22 15:37:18 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 15:37:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: <4C489DEE.1010806@bms.com> Chris, I tested tell and for me it actually returns the correct position. I think seek($fh, $start_pos, 0) || $self->throw("Failed resetting the filehandle pointer; IO error occurred"); might be better. On 7/22/2010 2:35 PM, Chris Fields wrote: > It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): > > tell() on pipes, fifos, and sockets usually returns -1. > > My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: > > if (!$self->seekable) { > #die a horrible death > } > > chris > > On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > > >> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). >> I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) >> I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. >> Another option is to right to a temp file or slurp into memory. This could be dangerous though... >> >> On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> >>> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >>> >>> -Aaron >>> >>> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov> wrote: >>> >>> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >>> >>> if (defined $self->{-file}) { >>> # Close the file we opened. >>> close($fh); >>> } elsif (ref $fh eq 'GLOB') { >>> # Try seeking to the start position. >>> >>> seek($fh, $start_pos, 0); >>> } elsif (defined $fh&& $fh->can('setpos')) { >>> # Seek to the start position. >>> $fh->setpos($start_pos); >>> } >>> return ($done ? $fmt_string : undef); >>> >>> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >>> after reset is where the second non-null line starts. >>> I am not sure why- all manuals claim this should work? >>> Hope this helps. >>> Stefan >>> >>> On 7/22/2010 9:27 AM, Chris Fields wrote: >>> >>> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> >>> $myseq->id,"\t",$myseq->seq,"\n"} >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >> >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From cjfields at illinois.edu Thu Jul 22 19:54:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 18:54:20 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? chris On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > Adding some more details on OS and BioPerl version > > OS: > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > UTC 2010 i686 GNU/Linux > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > BioPerl Version : > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > 'print $Bio::Root::Version::VERSION,"\n"' > 1.006001 > > Attached is the error that I get while running the RemoteBlast. > > Thanks, > Sheetal > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > wrote: > >> Hi, >> >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here >> is the complete script : >> #Remote-blast "factory object" creation and blast-parameter >> initialization >> >> use Bio::Tools::Run::RemoteBlast; >> use strict; >> my $prog = 'blastx'; >> my $db = 'nr/nt'; >> my $e_val= '1e-10'; >> >> my @params = ( '-prog' => $prog, >> '-data' => $db, >> '-expect' => $e_val, >> '-readmethod' => 'SearchIO' ); >> >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); >> >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; >> >> #$v is just to turn on and off the messages >> my $v = 0; >> >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' >> ); >> >> while (my $input = $str->next_seq()){ >> #Blast a sequence against a database: >> >> #Alternatively, you could pass in a file with many >> #sequences rather than loop through sequence one at a time >> #Remove the loop starting 'while (my $input = $str->next_seq())' >> #and swap the two lines below for an example of that. >> my $r = $factory->submit_blast($input); >> #my $r = $factory->submit_blast('amino.fa'); >> >> print STDERR "waiting..." if( $v > 0 ); >> while ( my @rids = $factory->each_rid ) { >> foreach my $rid ( @rids ) { >> my $rc = $factory->retrieve_blast($rid); >> if( !ref($rc) ) { >> if( $rc < 0 ) { >> print "removing rid as rc is < 0"; >> $factory->remove_rid($rid); >> } >> print STDERR "." if ( $v > 0 ); >> sleep 5; >> } else { >> my $result = $rc->next_result(); >> #save the output >> print "saving to file"; >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; >> $factory->save_output($filename); >> $factory->remove_rid($rid); >> print "\nQuery Name: ", $result->query_name(), "\n"; >> while ( my $hit = $result->next_hit ) { >> next unless ( $v > 0); >> print "\thit name is ", $hit->name, "\n"; >> while( my $hsp = $hit->next_hsp ) { >> print "\t\tscore is ", $hsp->score, "\n"; >> } >> } >> } >> } >> } >> } >> >> But when I run this, I get an error in html format which says "Cannot >> accept request, error code: -103". Attaching the error file for reference. >> Can you please help me with debugging this error? Your help is much >> appreciated. >> >> Also, informing about the previous error that I fixed by adding this line: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that >> I was getting prior to adding this line was : >> --------------------- WARNING --------------------- >> MSG:

An error has occurred on the >> server, The server is unable to format right now, please try again in a few >> minutes. If the problem (Informational Message: No alias or index file >> found for protein database [nr/nt] in search path >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: >> 4CF5MY9101P

>> >> It kinda took me a while to find out the 2 requirements >> >> # 1) set your database like this: >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options >> >> >> # 2) add this line before submitting the job: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; >> >> I think it will be great if you can add this to the synopsis section of >> RemoteBlast.pm >> >> Thanks, >> Sheetal >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Thu Jul 22 19:52:19 2010 From: genehack at genehack.org (John Anderson) Date: Thu, 22 Jul 2010 19:52:19 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: <4C487335.4080808@afrl.hpc.mil> References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: The one thing that sticks out is this: > Couldn't install Module::Build, giving up. Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. chrs, john. From cjfields at illinois.edu Thu Jul 22 21:53:36 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:53:36 -0500 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 6:52 PM, John Anderson wrote: > > On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: > > The one thing that sticks out is this: > >> Couldn't install Module::Build, giving up. > > Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. > > chrs, > john. Also helps to set any CPAN configuration to install locally. http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA chris From cjfields at illinois.edu Thu Jul 22 21:52:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:52:15 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Removing this line from your original script worked for me: $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; This is set via '-prog' parameter. chris On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". > > Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : > An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > Adding below the email conversation with blast-help for debugging further : > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: > Sheetal, > > You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. > > Best regards, > Wayne > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. > > The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. > > Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. > > Thanks, > Sheetal > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: > Hello, > > Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > Best regards, > Wayne > > _~___~___~__~__~_~ > Wayne Matten, PhD > NCBI Public Services > mattenw at mail.nih.gov > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > Hello, > > I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : > Cannot accept request, error code: -103 > > The request that I send is : > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx >> >> Can you please help me debug it. >> >> Thanks and Regards, >> Sheetal > > Thanks > Sheetal > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sheetu.piscean at gmail.com Thu Jul 22 20:30:24 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Thu, 22 Jul 2010 17:30:24 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. Adding below the email conversation with blast-help for debugging further : On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: Sheetal, You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. Best regards, Wayne http://www.ncbi.nlm.nih.gov/blast /Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. Thanks, Sheetal On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: Hello, Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo Best regards, Wayne _~___~___~__~__~_~ Wayne Matten, PhD NCBI Public Services mattenw at mail.nih.gov On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: Hello, I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : Cannot accept request, error code: -103 The request that I send is : POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx Can you please help me debug it. Thanks and Regards, Sheetal Thanks Sheetal On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version > -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for > reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this > line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a > few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From shachigahoimbi at gmail.com Fri Jul 23 07:01:01 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:31:01 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From shachigahoimbi at gmail.com Fri Jul 23 07:28:05 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:58:05 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From giles.weaver at bbsrc.ac.uk Fri Jul 23 07:31:11 2010 From: giles.weaver at bbsrc.ac.uk (Giles Weaver) Date: Fri, 23 Jul 2010 12:31:11 +0100 Subject: [Bioperl-l] bioperl modules In-Reply-To: References: Message-ID: <4C497D7F.1060806@bbsrc.ac.uk> See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. Regards, Giles On 23/07/10 12:01, Shachi Gahoi wrote: > I want to use following bioperl modules. I have installed bioperl 1.6.I. > have searched all modules in it but i have not found following modules. I > want to use it. please tell me if anyone know about these modules and use of > it. > > temp- for temperature checking > ac- for count of AC content > gc- for count of GC content > dimer- check bases for dimerization > check 5- Check the presence of GC, CG, C or G at 5' > check 3- Check the presence of GC, CG, C or G at 3' > basepair- calculate % of GC > hairpin- calculate hairpin structure > delta- calculate delta G value for primer > temp diff- check for temperature difference in left and right primer > > please tell me if anyone know about these modules. > > Thanks in advance > > > From cjfields at illinois.edu Fri Jul 23 09:17:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 08:17:41 -0500 Subject: [Bioperl-l] bioperl modules In-Reply-To: <4C497D7F.1060806@bbsrc.ac.uk> References: <4C497D7F.1060806@bbsrc.ac.uk> Message-ID: <688164AF-AF7B-49D0-9E68-A4916C7A2DDC@illinois.edu> This sounds suspiciously like homework, so I'm reluctant to give any direct answers. Most (all?) of these are covered in the Tisdall books, IIRC, and all use regexes or transliteration, that's about all I'll say. chris On Jul 23, 2010, at 6:31 AM, Giles Weaver wrote: > See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. > Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. > > Regards, > > Giles > > On 23/07/10 12:01, Shachi Gahoi wrote: >> I want to use following bioperl modules. I have installed bioperl 1.6.I. >> have searched all modules in it but i have not found following modules. I >> want to use it. please tell me if anyone know about these modules and use of >> it. >> >> temp- for temperature checking >> ac- for count of AC content >> gc- for count of GC content >> dimer- check bases for dimerization >> check 5- Check the presence of GC, CG, C or G at 5' >> check 3- Check the presence of GC, CG, C or G at 3' >> basepair- calculate % of GC >> hairpin- calculate hairpin structure >> delta- calculate delta G value for primer >> temp diff- check for temperature difference in left and right primer >> >> please tell me if anyone know about these modules. >> >> Thanks in advance >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From pg4 at sanger.ac.uk Fri Jul 23 04:06:38 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 09:06:38 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' Message-ID: Hello, Regarding the recent post about installing bioperl as non root, http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique http://perl.jonallen.info/writing/articles/install-perl-modules-without-root I wanted to put it in the talk page first, but there is an 'issue': The talk link points to http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix Talk:Installing Bioperl for Unix 2 and in this talk page, the page link point to a deleted page http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 Editing Installing Bioperl for Unix 2 Warning: You are recreating a page that was previously deleted. You should consider whether it is appropriate to continue editing this page. The deletion log for this page is provided here for convenience: * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing Bioperl for Unix 2" ? (testing out page (adding back from file)) Just to let you know. ----- Pablo Marin-Garcia -- 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 Fri Jul 23 11:07:23 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 10:07:23 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: Message-ID: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Pablo, No idea how that happened, but I removed the older discussion page and my obsolete comment, along with the redirect on the main discussion page. Edit away! chris On Jul 23, 2010, at 3:06 AM, Pablo Marin-Garcia wrote: > Hello, > > Regarding the recent post about installing bioperl as non root, > > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. > > http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique > http://perl.jonallen.info/writing/articles/install-perl-modules-without-root > > I wanted to put it in the talk page first, but there is an 'issue': > > The talk link points to > http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix > Talk:Installing Bioperl for Unix 2 > > and in this talk page, the page link point to a deleted page > http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 > > Editing Installing Bioperl for Unix 2 > Warning: You are recreating a page that was previously deleted. > > You should consider whether it is appropriate to continue editing this page. > The deletion log for this page is provided here for convenience: > > * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing > Bioperl > for Unix 2" ? (testing out page (adding back from file)) > > > Just to let you know. > > ----- > > Pablo Marin-Garcia > > > > -- > 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. > _______________________________________________ > 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 Fri Jul 23 11:42:09 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 09:42:09 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: Thanks for that addition to the wiki, Pablo! Much appreciated. I did not know about local::lib. Dave From pg4 at sanger.ac.uk Fri Jul 23 12:52:03 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 17:52:03 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Dave Messina wrote: > Thanks for that addition to the wiki, Pablo! Much appreciated. > > I did not know about local::lib. > [This is a bit off-topic but probably useful for core developers] Then probably you don't know about App::perlbrew Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ---- Copied from the SYNOPSIS: # Initialize perlbrew init # Install some Perls perlbrew install perl-5.8.1 perlbrew install perl-5.11.5 # See what were installed perlbrew installed # Switch perl in the $PATH perlbrew switch perl-5.11.5 perl -v # Switch to another version perlbrew switch perl-5.8.1 perl -v # Switch to a certain perl executable not managed by perlbrew. perlbrew switch /usr/bin/perl # Or turn it off completely. Useful when you messed up too deep. perlbrew off # Use 'switch' command to turn it back on. perlbrew switch perl-5.11.5 -Pablo > > Dave > ----- Pablo Marin-Garcia -- 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 Fri Jul 23 12:57:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 11:57:05 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ... yes, just started using this myself. Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. chris From cjfields at illinois.edu Fri Jul 23 13:01:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:01:20 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ...and completely forgot to mention the tremendous benefits of App::perlbrew for development! Lots of very nice tools becoming available these days... chris From cjfields at illinois.edu Fri Jul 23 13:20:44 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:20:44 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> http://github.com/cjfields/bioperl6 http://github.com/cjfields/biome :) chris On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > > extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: > > http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html > > I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. > > > Have a good weekend > > -Pablo > > > > On Fri, 23 Jul 2010, Chris Fields wrote: > >> >> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >> >>> On Fri, 23 Jul 2010, Dave Messina wrote: >>> >>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>> >>>> I did not know about local::lib. >>>> >>> >>> [This is a bit off-topic but probably useful for core developers] >>> Then probably you don't know about >>> >>> App::perlbrew >>> >>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >> ... >> >> yes, just started using this myself. >> >> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >> >> chris > > > ----- > > Pablo Marin-Garcia > > > > -- > 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 sheetu.piscean at gmail.com Fri Jul 23 13:04:59 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 10:04:59 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: I did remove that line but doesn't help. I still keep getting this error: MSG:

An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4KJE1YJ601N

Any pointers ?? - Sheetal On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > This is set via '-prog' parameter. > > chris > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to Blast-help as well > and they have to say that "there is something wrong with the URL, didn't > give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default it is set to > plain, I guess this value is for standard blast pgm. like blastp, blastx, > etc) gives me this error : > > An error has occurred on the server, The server is unable to format right > now, please try again in a few minutes. If the problem (Informational > Message: No alias or index file found for protein database [nr/nt] in search > path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for debugging further > : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some errors. The > URL below works; note that order of parameters does not matter. > > > > Best regards, > > Wayne > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning immediately after > "QUERY=", (called as bare sequence) but still I get the same error. > > > > The documentation on your URLAPI says that Query can have Accession(s), > gi(S) or FASTA sequence. The format of the query for FASTA sequence is as > shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA > sequence, the query has description/definition followed by actual sequence. > In that case, the format of my POST request match the requirement. > > > > Can you help me figure out why am I still getting error : "Cannot accept > request, error code: -103" ? Attaching the log file having Query as bare > sequence and FASTA sequence for your reference. Your help is much > appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not use, requires > that the sequence begin immediately after "QUERY=". Your example shows a > definition line preceding the sequence. You can get documentation on our > URLAPI on this page (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my Bioperl script > remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded > DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 > 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a time > > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; > #$result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which says "Cannot > > >> accept request, error code: -103". Attaching the error file for > reference. > > >> Can you please help me with debugging this error? Your help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by adding this > line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has occurred on > the > > >> server, The server is unable to format right now, please try again in > a few > > >> minutes. If the problem (Informational Message: No alias or index > file > > >> found for protein database [nr/nt] in search path > > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the synopsis section > of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > From pg4 at sanger.ac.uk Fri Jul 23 13:17:50 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:17:50 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. Have a good weekend -Pablo On Fri, 23 Jul 2010, Chris Fields wrote: > > On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > >> On Fri, 23 Jul 2010, Dave Messina wrote: >> >>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>> >>> I did not know about local::lib. >>> >> >> [This is a bit off-topic but probably useful for core developers] >> Then probably you don't know about >> >> App::perlbrew >> >> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. > ... > > yes, just started using this myself. > > Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. > > chris ----- Pablo Marin-Garcia -- 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 Fri Jul 23 13:36:40 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:36:40 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> I've attached the code and example data that worked. This is using the latest bioperl on github, so maybe it's the version you have installed? chris On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > I did remove that line but doesn't help. I still keep getting this > error: > MSG:

An error has occurred on > the server, The server is unable to format right now, please try again > in a few minutes. If the problem (Informational Message: No alias or > index file found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4KJE1YJ601N

> > Any pointers ?? > > - Sheetal > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > This is set via '-prog' parameter. > > chris > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to > Blast-help as well and they have to say that "there is > something wrong with the URL, didn't give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default > it is set to plain, I guess this value is for standard blast > pgm. like blastp, blastx, etc) gives me this error : > > An error has occurred on the server, The server is unable to > format right now, please try again in a few minutes. If the > problem (Informational Message: No alias or index file found > for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for > debugging further : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some > errors. The URL below works; note that order of parameters > does not matter. > > > > Best regards, > > Wayne > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > 3EContig_236+%0A% > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning > immediately after "QUERY=", (called as bare sequence) but > still I get the same error. > > > > The documentation on your URLAPI says that Query can have > Accession(s), gi(S) or FASTA sequence. The format of the query > for FASTA sequence is as shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > for FASTA sequence, the query has description/definition > followed by actual sequence. In that case, the format of my > POST request match the requirement. > > > > Can you help me figure out why am I still getting error : > "Cannot accept request, error code: -103" ? Attaching the log > file having Query as bare sequence and FASTA sequence for your > reference. Your help is much appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not > use, requires that the sequence begin immediately after > "QUERY=". Your example shows a definition line preceding the > sequence. You can get documentation on our URLAPI on this page > (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my > Bioperl script remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > 3EContig_236+% > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI > server, not problems with the script. Is this still > occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > Jun 11 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the > RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on > 'nr' database. Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and > blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > -format => 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a > time > > >> #Remove the loop starting 'while (my $input = > $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; # > $result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), > "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which > says "Cannot > > >> accept request, error code: -103". Attaching the error > file for reference. > > >> Can you please help me with debugging this error? Your > help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by > adding this line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; The error that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has > occurred on the > > >> server, The server is unable to format right now, please > try again in a few > > >> minutes. If the problem (Informational Message: No > alias or index file > > >> found for protein database [nr/nt] in search path > > >> > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 > requirements > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the > synopsis section of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: test.pl Type: application/x-perl Size: 2211 bytes Desc: not available URL: -------------- next part -------------- >Foo My description here AATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGG CGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGA GGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCT CCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCC ACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAG AAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCAT GGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAAT GCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCC TGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCG GGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGA TTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGC CCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAG CCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAAT CCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGG CTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTAT ACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCT CAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGC GCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACG CAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTG TCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTC AGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGAT GAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTG CGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCAC GCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGA GACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACT CAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCA TCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAAC AGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAG CGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTT CTGT From pg4 at sanger.ac.uk Fri Jul 23 13:33:10 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:33:10 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Chris Fields wrote: > http://github.com/cjfields/bioperl6 oh, very nice!. > http://github.com/cjfields/biome one of my to-do things for my holidays is to git clone it and star to play with it. I have several mOOse modules for GWAS that I am going to release soon but I would like to accomodate them first to the bioperl look and feel. > :) > > chris > > On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > >> >> extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: >> >> http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html >> >> I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. >> >> >> Have a good weekend >> >> -Pablo >> >> >> >> On Fri, 23 Jul 2010, Chris Fields wrote: >> >>> >>> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >>> >>>> On Fri, 23 Jul 2010, Dave Messina wrote: >>>> >>>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>>> >>>>> I did not know about local::lib. >>>>> >>>> >>>> [This is a bit off-topic but probably useful for core developers] >>>> Then probably you don't know about >>>> >>>> App::perlbrew >>>> >>>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >>> ... >>> >>> yes, just started using this myself. >>> >>> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >>> >>> chris >> >> >> ----- >> >> Pablo Marin-Garcia >> >> >> >> -- >> 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. > > ----- Pablo Marin-Garcia -- 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 sheetu.piscean at gmail.com Fri Jul 23 14:15:51 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 11:15:51 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> References: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> Message-ID: Thanks a lot Chris. It worked for me as well :) - Sheetal On Fri, Jul 23, 2010 at 10:36 AM, Chris Fields wrote: > I've attached the code and example data that worked. This is using the > latest bioperl on github, so maybe it's the version you have installed? > > chris > > On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > > I did remove that line but doesn't help. I still keep getting this > > error: > > MSG:

An error has occurred on > > the server, The server is unable to format right now, please try again > > in a few minutes. If the problem (Informational Message: No alias or > > index file found for protein database [nr/nt] in search path > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > 4KJE1YJ601N

> > > > Any pointers ?? > > > > - Sheetal > > > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > > wrote: > > Removing this line from your original script worked for me: > > > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > > > > This is set via '-prog' parameter. > > > > chris > > > > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > > > Yes the error is still occurring. I have emailed to > > Blast-help as well and they have to say that "there is > > something wrong with the URL, didn't give any specifics". > > > > > > Also changing the parameter SERVICE to 'plain' (by default > > it is set to plain, I guess this value is for standard blast > > pgm. like blastp, blastx, etc) gives me this error : > > > An error has occurred on the server, The server is unable to > > format right now, please try again in a few minutes. If the > > problem (Informational Message: No alias or index file found > > for protein database [nr/nt] in search path > > > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I > have sent an email today to blast-help for this error. > > > > > > Adding below the email conversation with blast-help for > > debugging further : > > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > > wrote: > > > Sheetal, > > > > > > You are right about the query syntax, but your URL has some > > errors. The URL below works; note that order of parameters > > does not matter. > > > > > > Best regards, > > > Wayne > > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > > 3EContig_236+%0A% > > > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > > > Thank you Wayne. I tried with the sequence beginning > > immediately after "QUERY=", (called as bare sequence) but > > still I get the same error. > > > > > > The documentation on your URLAPI says that Query can have > > Accession(s), gi(S) or FASTA sequence. The format of the query > > for FASTA sequence is as shown: > > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > > for FASTA sequence, the query has description/definition > > followed by actual sequence. In that case, the format of my > > POST request match the requirement. > > > > > > Can you help me figure out why am I still getting error : > > "Cannot accept request, error code: -103" ? Attaching the log > > file having Query as bare sequence and FASTA sequence for your > > reference. Your help is much appreciated. > > > > > > Thanks, > > > Sheetal > > > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > > wrote: > > > Hello, > > > > > > Our URLAPI, which your script should, but may or may not > > use, requires that the sequence begin immediately after > > "QUERY=". Your example shows a definition line preceding the > > sequence. You can get documentation on our URLAPI on this page > > (Web service interface): > > > > > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > > > Best regards, > > > Wayne > > > > > > _~___~___~__~__~_~ > > > Wayne Matten, PhD > > > NCBI Public Services > > > mattenw at mail.nih.gov > > > > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > Hello, > > > > > > I am trying to use blastx program with 'nr' database in my > > Bioperl script remotely. While I do so, I get this error : > > > Cannot accept request, error code: -103 > > > > > > The request that I send is : > > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > > bioperl-Bio_Tools_Run_ > > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > > 3EContig_236+% > > > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > > >> > > >> Can you please help me debug it. > > >> > > >> Thanks and Regards, > > >> Sheetal > > > > > > Thanks > > > Sheetal > > > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > > wrote: > > > The errors reported seem to indicate problems on the NCBI > > server, not problems with the script. Is this still > > occurring? > > > > > > chris > > > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > > Adding some more details on OS and BioPerl version > > > > > > > > OS: > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > > Jun 11 07:54:58 > > > > UTC 2010 i686 GNU/Linux > > > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > > > BioPerl Version : > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > > -MBio::Root::Version -e > > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > > 1.006001 > > > > > > > > Attached is the error that I get while running the > > RemoteBlast. > > > > > > > > Thanks, > > > > Sheetal > > > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > > wrote: > > > > > > > >> Hi, > > > >> > > > >> I am trying to run RemoteBlast to blastx sequences on > > 'nr' database. Here > > > >> is the complete script : > > > >> #Remote-blast "factory object" creation and > > blast-parameter > > > >> initialization > > > >> > > > >> use Bio::Tools::Run::RemoteBlast; > > > >> use strict; > > > >> my $prog = 'blastx'; > > > >> my $db = 'nr/nt'; > > > >> my $e_val= '1e-10'; > > > >> > > > >> my @params = ( '-prog' => $prog, > > > >> '-data' => $db, > > > >> '-expect' => $e_val, > > > >> '-readmethod' => 'SearchIO' ); > > > >> > > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > > >> > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; > > > >> > > > >> #$v is just to turn on and off the messages > > > >> my $v = 0; > > > >> > > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > > -format => 'fasta' > > > >> ); > > > >> > > > >> while (my $input = $str->next_seq()){ > > > >> #Blast a sequence against a database: > > > >> > > > >> #Alternatively, you could pass in a file with many > > > >> #sequences rather than loop through sequence one at a > > time > > > >> #Remove the loop starting 'while (my $input = > > $str->next_seq())' > > > >> #and swap the two lines below for an example of that. > > > >> my $r = $factory->submit_blast($input); > > > >> #my $r = $factory->submit_blast('amino.fa'); > > > >> > > > >> print STDERR "waiting..." if( $v > 0 ); > > > >> while ( my @rids = $factory->each_rid ) { > > > >> foreach my $rid ( @rids ) { > > > >> my $rc = $factory->retrieve_blast($rid); > > > >> if( !ref($rc) ) { > > > >> if( $rc < 0 ) { > > > >> print "removing rid as rc is < 0"; > > > >> $factory->remove_rid($rid); > > > >> } > > > >> print STDERR "." if ( $v > 0 ); > > > >> sleep 5; > > > >> } else { > > > >> my $result = $rc->next_result(); > > > >> #save the output > > > >> print "saving to file"; > > > >> my $filename = "contig_236.out"; # > > $result->query_name()."\.out"; > > > >> $factory->save_output($filename); > > > >> $factory->remove_rid($rid); > > > >> print "\nQuery Name: ", $result->query_name(), > > "\n"; > > > >> while ( my $hit = $result->next_hit ) { > > > >> next unless ( $v > 0); > > > >> print "\thit name is ", $hit->name, "\n"; > > > >> while( my $hsp = $hit->next_hsp ) { > > > >> print "\t\tscore is ", $hsp->score, "\n"; > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> > > > >> But when I run this, I get an error in html format which > > says "Cannot > > > >> accept request, error code: -103". Attaching the error > > file for reference. > > > >> Can you please help me with debugging this error? Your > > help is much > > > >> appreciated. > > > >> > > > >> Also, informing about the previous error that I fixed by > > adding this line: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; The error that > > > >> I was getting prior to adding this line was : > > > >> --------------------- WARNING --------------------- > > > >> MSG:

An error has > > occurred on the > > > >> server, The server is unable to format right now, please > > try again in a few > > > >> minutes. If the problem (Informational Message: No > > alias or index file > > > >> found for protein database [nr/nt] in search path > > > >> > > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > > RID: > > > >> 4CF5MY9101P

> > > >> > > > >> It kinda took me a while to find out the 2 > > requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > > >> > > > >> # 1) set your database like this: > > > >> -database => 'cdsearch/cdd', # c.f. > > > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > > >> > > > >> > > > >> # 2) add this line before submitting the job: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'rpsblast'; > > > >> > > > >> I think it will be great if you can add this to the > > synopsis section of > > > >> RemoteBlast.pm > > > >> > > > >> Thanks, > > > >> Sheetal > > > >> > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > From y-bushmanova at northwestern.edu Fri Jul 23 14:54:19 2010 From: y-bushmanova at northwestern.edu (Yulia Bushmanova) Date: Fri, 23 Jul 2010 13:54:19 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E26F.4020103@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> Message-ID: <4C49E55B.6000509@northwestern.edu> Sorry, first email had wrong file attached Yulia Yulia Bushmanova wrote: > Hi All, > > I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and > got following error: > > not well-formed (invalid token) at line 32, column 48, byte 3095 at > /usr/lib/perl5/XML/Parser.pm line 187 > > Looks like parser complains on the copyright sign, if I manually > remove it from file parsing goes fine. XML::Parser is version 2.36. > > Any ideas on how to deal with this error? > > Thanks in advance, > Yulia -------------- next part -------------- A non-text attachment was scrubbed... Name: allRefs_07232010.xml Type: text/xml Size: 42911 bytes Desc: not available URL: From David.Messina at sbc.su.se Fri Jul 23 15:00:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 13:00:07 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> Message-ID: <9C35A675-7A6C-4A33-8826-443CD4E5E541@sbc.su.se> Cool, thanks for the pointer to perlbrew! Dave From cjfields at illinois.edu Fri Jul 23 15:08:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 14:08:03 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E55B.6000509@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> <4C49E55B.6000509@northwestern.edu> Message-ID: <105D6D53-1465-44ED-BA6A-B2D642F09BA9@illinois.edu> You should file this as a bug, along with the output. My guess is it has to do with character encoding, but not sure. chris On Jul 23, 2010, at 1:54 PM, Yulia Bushmanova wrote: > Sorry, first email had wrong file attached > > Yulia > > Yulia Bushmanova wrote: >> Hi All, >> >> I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and got following error: >> >> not well-formed (invalid token) at line 32, column 48, byte 3095 at /usr/lib/perl5/XML/Parser.pm line 187 >> >> Looks like parser complains on the copyright sign, if I manually remove it from file parsing goes fine. XML::Parser is version 2.36. >> >> Any ideas on how to deal with this error? >> >> Thanks in advance, >> Yulia > > > > > > > 20643054 > > 2010 > 7 > 20 > >
> > 1542-0086 > > 99 > 2 > > 2010 > Jul > 21 > > > Biophysical journal > > Bimodal Analysis Reveals a General Scaling Law Governing Nondirected and Chemotactic Cell Motility. > > 367-376 > > > Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a nondirected fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses. Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multiscale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both nondirected and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines, indicating that the coupling of reorientation and persistence holds across species and making it possible to describe the complexity of cell motility in a surprisingly general and simple manner. With this new perspective, we analyzed the motility of Dictyostelium mutants, and found four in which the coupling between two modes was altered. Our results point to a fundamental underlying principle, described by a simple scaling law, unifying mechanisms of eukaryotic cell motility at several scales. > Copyright ? 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. > > Department of Pharmacology, Vanderbilt University, Nashville, Tennessee. > > > Gruver > J Scott > JS > > > Potdar > Alka A > AA > > > Jeon > Junhwan > J > > > Sai > Jiqing > J > > > Anderson > Bridget > B > > > Webb > Donna > D > > > Richmond > Ann > A > > > Quaranta > Vito > V > > > Cummings > Peter T > PT > > > Chung > Chang Y > CY > > > ENG > > JOURNAL ARTICLE > >
> > Biophys J > 0370626 > 0006-3495 > > > > > > 2009 > 12 > 17 > > > 2010 > 3 > 9 > > > 2010 > 3 > 11 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > ppublish > > S0006-3495(10)00710-1 > 10.1016/j.bpj.2010.03.073 > 20643054 > > > > > > > > 20640912 > > 2010 > 7 > 19 > >
> > 1420-9071 > > > 2010 > Jul > 18 > > > Cellular and molecular life sciences : CMLS > > Redundant and unique roles of coronin proteins in Dictyostelium. > > > > > Dictyostelium discoideum harbors a short (CRN12) and a long coronin (CRN7) composed of one and two beta-propellers, respectively. They are primarily present in the cell cortex and cells lacking CRN12 (corA (-)) or CRN7 (corB (-)) have defects in actin driven processes. We compared the characteristics of a mutant cell line (corA (-) /corB (-)) lacking CRN12 and CRN7 with the single mutants focusing on cytokinesis, phagocytosis, chemotaxis and development. Cytokinesis, uptake of small particles, and developmental defects were not enhanced in the corA (-) /corB (-) strain as compared to the single mutants, whereas motility and phagocytosis of yeast particles were more severely impaired. It appears that although both proteins affect the same processes they do not act in a redundant manner. Rather, they often act antagonistically, which is in accordance with their proposed roles in the actin cytoskeleton where CRN12 acts in actin disassembly whereas CRN7 stabilizes actin filaments and protects them from disassembly. > > Institute for Biochemistry I, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931, Cologne, Germany. > > > Shina > Maria C > MC > > > M?ller-Taubenberger > Annette > A > > > Unal > Can > C > > > Schleicher > Michael > M > > > Steinert > Michael > M > > > Eichinger > Ludwig > L > > > M?ller > Rolf > R > > > Blau-Wasser > Rosemarie > R > > > Gl?ckner > Gernot > G > > > Noegel > Angelika A > AA > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 18 > >
> > Cell Mol Life Sci > 9705402 > 1420-682X > > > > > > 2010 > 2 > 3 > > > 2010 > 7 > 5 > > > 2010 > 5 > 23 > > > 2010 > 7 > 18 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 10.1007/s00018-010-0455-y > 20640912 > > > > > > > > 20639697 > > 2010 > 7 > 19 > >
> > 1554-8635 > > 6 > 6 > > 2010 > Aug > 22 > > > Autophagy > > A second signal for autophagic cell death? > > > > > Dictyostelium cells in monolayers in vitro lend themselves well to a study of autophagic cell death (ACD). There is no apoptosis machinery in the protist Dictyostelium, no caspase nor Bcl-2 family members (except a paracaspase whose inactivation does not alter cell death), thus there is no apoptosis that could interfere with, or substitute for, nonapoptotic cell death. Also, Dictyostelium, a eukaryote, has a haploid genome, which facilitates random insertional mutagenesis. > > Centre d'Immunologie de Marseille-Luminy, Facult? des Sciences de Luminy, Aix Marseille Universit?, Marseille, France; Institut National de la Sant? et de la Recherche M?dicale U631, Marseille, France; Centre National de la Recherche Scientifique Unit? Mixte de Recherche, Marseille, France. > > > Giusti > Corinne > C > > > Luciani > Marie-Fran?oise > MF > > > Golstein > Pierre > P > > > ENG > > JOURNAL ARTICLE > > > 2010 > 8 > 22 > >
> > Autophagy > 101265188 > 1554-8627 > > > > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 12750 > 20639697 > > > > > > > > 20626455 > > 2010 > 7 > 19 > >
> > 1462-2920 > > > 2010 > Jul > 7 > > > Environmental microbiology > > The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa. > > > > > Summary The capacity of a bacterial pathogen to produce a disease in a treated host depends on the former's virulence and resistance to antibiotics. Several scattered pieces of evidence suggest that these two characteristics can be influenced by bacterial metabolism. This potential relationship is particularly important upon infection of a host, a situation that demands bacteria adapt their physiology to their new environment, making use of newly available nutrients. To explore the potential cross-talk between bacterial metabolism, antibiotic resistance and virulence, a Pseudomonas aeruginosa model was used. This species is an important opportunistic pathogen intrinsically resistant to many antibiotics. The role of Crc, a global regulator that controls the metabolism of carbon sources and catabolite repression in Pseudomonas, was analysed to determine its contribution to the intrinsic antibiotic resistance and virulence of P. aeruginosa. Using proteomic analyses, high-throughput metabolic tests and functional assays, the present work shows the virulence and antibiotic resistance of this pathogen to be linked to its physiology, and to be under the control (directly or indirectly) of Crc. A P. aeruginosa strain lacking the Crc regulator showed defects in type III secretion, motility, expression of quorum sensing-regulated virulence factors, and was less virulent in a Dictyostelium discoideum model. In addition, this mutant strain was more susceptible to beta-lactams, aminoglycosides, fosfomycin and rifampin. Crc might therefore be a good target in the search for new antibiotics. > > Departamento de Biotecnolog?a Microbiana, Centro Nacional de Biotecnolog?a, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain. > > > Linares > Juan F > JF > > > Moreno > Renata > R > > > Fajardo > Alicia > A > > > Mart?nez-Solano > Laura > L > > > Escalante > Ricardo > R > > > Rojo > Fernando > F > > > Mart?nez > Jos? L > JL > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 07 > >
> > Environ Microbiol > 100883692 > 1462-2912 > > > > > > 2010 > 7 > 15 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > aheadofprint > > EMI2292 > 10.1111/j.1462-2920.2010.02292.x > 20626455 > > > > > > > > 20624437 > > 2010 > 7 > 20 > >
> > 1873-5169 > > > 2010 > Jul > 16 > > > Peptides > > Synthesis and biological activity of peptides equivalent to the IP22 repeat motif found in proteins from Dictyostelium and Mimivirus. > > > > > A novel IP22 repeat motif of unknown function was discovered previously that comprises almost the entire structure of cmbB, a calmodulin-binding protein from Dictyostelium discoideum. An analysis of over 2000 IP22 repeats across 130 different proteins from different species allowed us to define a prototypical IP22 repeat: I/LPxxhxxhxhxxxhxxxhxxxx (where L=leucine, I=isoleucine, h=any hydrophobic amino acid, x=any amino acid). Here we describe the synthesis of three peptide variants of the IP22 motif: IP22-1 (IPNSVTSLKFGDGFNQPLTPGT; 22aa); IP22-2 (LPSTLKTISLSNSTDKKIFKNS; 22aa); and, IP22-3 (IPKSLRSLFLGKGYNQPLEF; 20aa) plus a control peptide from the N-term of cmbB (HNMNPFSPQLDEKKNSHIVEY; 21aa). The structure and purity of synthesized peptides were verified by HPLC and mass spectrometry. The peptides all dose-dependently enhanced random cell motility and cAMP-mediated chemotaxis in Dictyostelium but IP22-3 was most effective peaking in activity around 50muM. Fluorescein isothiocyanate (FITC)-conjugated IP22 peptides did not penetrate cells suggesting these peptides affect cell motility via cell surface interactions. Treatment of cells with FITC-IP22 peptides also led to enhanced cell motility equivalent to the non-conjugated peptides. Treatment of IP22-3-stimulated cells with 50muM LY294002, 20muM quinacrine or both suggests that IP22-3 requires both phosphoinositol 3-kinase and phospholipase A2 signaling to elicit its effects, a mechanism unique from EGFL motility enhancing peptides. The mechanism of action and potential uses of IP22 repeat peptides are discussed. > Copyright ? 2010. Published by Elsevier Inc. > > Department of Cell and Systems Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada, L5L 1C6; Department of Biology, University of Toronto at Mississauga, 3359 Mississauga rd. N., Mississauga, Ontario, Canada, L5L 1C6. > > > Catalano > Andrew > A > > > Luo > Wei > W > > > Wang > Yali > Y > > > O'Day > Danton H > DH > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 16 > >
> > Peptides > 8008690 > 0196-9781 > > > > > > 2010 > 6 > 22 > > > 2010 > 7 > 3 > > > 2010 > 7 > 5 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > aheadofprint > > S0196-9781(10)00300-1 > 10.1016/j.peptides.2010.07.005 > 20624437 > > > > > > > > 20617172 > > 2010 > 07 > 09 > >
> > 1553-7404 > > 6 > > 2010 > > > PLoS genetics > PLoS Genet. > > Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum. > > e1001013 > > > Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle. > > Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America. > > > Flowers > Jonathan M > JM > > > Li > Si I > SI > > > Stathos > Angela > A > > > Saxer > Gerda > G > > > Ostrowski > Elizabeth A > EA > > > Queller > David C > DC > > > Strassmann > Joan E > JE > > > Purugganan > Michael D > MD > > > eng > > Journal Article > Research Support, U.S. Gov't, Non-P.H.S. > > > 2010 > 07 > 01 > >
> > United States > PLoS Genet > 101239074 > 1553-7390 > > IM > PMC2895654 > > > > > 2010 > 3 > 15 > > > 2010 > 6 > 1 > > > 2010 > 7 > 1 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > epublish > > 10.1371/journal.pgen.1001013 > 20617172 > PMC2895654 > > > > > > > > 20610381 > > 2010 > 7 > 8 > >
> > 1083-351X > > > 2010 > Jul > 7 > > > The Journal of biological chemistry > > Expression of actin Tyr53Ala in Dictyostelium disrupts the cytoskeleton and inhibits intracellular and intercellular chemotactic-signaling. > > > > > We showed previously that phosphorylation of Tyr-53, or its mutation to Ala, inhibits actin polymerization in vitro with formation of aggregates of short filaments, and that expression of Y53A-actin in Dictyostelium blocks differentiation and development at the mound stage (Liu et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13694-13699; Liu et al. (2010) J. Biol. Chem. 285, 9729-9739). We now show that expression of Y53A-actin, which does not affect cell growth, phagocytosis or pinocytosis, inhibits the formation of head-to-tail cell streams during cAMP-induced aggregation, although individual amoebae chemotax normally. We show that expression of Y53A-actin causes a 50% reduction of cell-surface cAMP-receptors, and inhibits cAMP-induced increases in adenylyl cyclase A activity, phosphorylation of ERK2 and actin polymerization. Trafficking of vesicles containing adenylyl cyclase A to the rear of the cell and secretion of the ACA-vesicles are also inhibited. The actin cytoskeleton of cells expressing Y53A-actin is characterized by numerous short filaments, and bundled and aggregated filaments similar to the structures formed by copolymerization of purified Y53A-actin and wild-type actin in vitro. This disorganized actin cytoskeleton may be responsible for the inhibition of intracellular and intercellular cAMP signaling in cells expressing F-Y/A-actin. > > NHLBI, NIH, United States; > > > Shu > Shi > S > > > Liu > Xiong > X > > > Kriebel > Paul W > PW > > > Hong > Myoung-Soon > MS > > > Daniels > Mathew P > MP > > > Parent > Carole A > CA > > > Korn > Edward D > ED > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 7 > >
> > J Biol Chem > 2985121R > 0021-9258 > > > > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > aheadofprint > > M110.116277 > 10.1074/jbc.M110.116277 > 20610381 > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Fri Jul 23 19:04:38 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 23 Jul 2010 19:04:38 -0400 Subject: [Bioperl-l] reroot looses branch information Message-ID: Hi, I'm playing with some tree methods from Bio::Tree::TreeFunctionI and I found that Bio::Tree::TreeFunctionI::reroot looses the bootstrap support for the branch leading to the ancestor of the new root. Therefore, when calling reroot, I'm using code like my $ancestor = $newroot->ancestor; my $support = $newroot->bootstrap if (defined $ancestor); $tree->reroot($newroot); $ancestor->bootstrap($support) if (defined $support && defined $ancestor); There seems to be some code in reroot() to prevent that but I don't know why this is happening... Could you please check and fix that? Cheers, Robson From jason.stajich at gmail.com Sat Jul 24 12:41:30 2010 From: jason.stajich at gmail.com (Jason Stajich) Date: Sat, 24 Jul 2010 09:41:30 -0700 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <1125612054.776980.1279892924891.JavaMail.root@zimbra> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> Message-ID: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Hi. You should ask questions to the list. There are many who can answer your question there. In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. -Jason. Sent from my iPod On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > Hi Jason Stajich, > > I am using Bioperl and it is very useful. I have a question about > Bio::DB::GenBank. > This is a simple code. > > -------------------------- > > $db = Bio::DB::GenBank->new(); > @ids = ("LOC441435", "X78121"); > foreach $id (@ids){ > $seqobj = $db->get_Seq_by_id($id); > $seqstr = $seqobj->seq(); > print "$>id\n$seqstr\n"; > } > > -------------------------- > > If there is no entry for an ID, I would like to skip it and to get > next one. But this code stops running when an ID does not exist in > genbank. > How can I solve this problem? > > Thanks. > Hongseok Tae > From cjfields at illinois.edu Sat Jul 24 13:00:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 24 Jul 2010 12:00:24 -0500 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Message-ID: <9F83881D-6C9C-4996-95DF-D98C140DC3EB@illinois.edu> Any reason not to use a stream here? my $io = $db->get_Stream_by_id(\@ids); while (my $seq = $stream->next_seq) { # do stuff here } chris On Jul 24, 2010, at 11:41 AM, Jason Stajich wrote: > Hi. You should ask questions to the list. There are many who can answer your question there. > > In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. > > You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. > -Jason. > Sent from my iPod > > On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > >> Hi Jason Stajich, >> >> I am using Bioperl and it is very useful. I have a question about Bio::DB::GenBank. >> This is a simple code. >> >> -------------------------- >> >> $db = Bio::DB::GenBank->new(); >> @ids = ("LOC441435", "X78121"); >> foreach $id (@ids){ >> $seqobj = $db->get_Seq_by_id($id); >> $seqstr = $seqobj->seq(); >> print "$>id\n$seqstr\n"; >> } >> >> -------------------------- >> >> If there is no entry for an ID, I would like to skip it and to get next one. But this code stops running when an ID does not exist in genbank. >> How can I solve this problem? >> >> Thanks. >> Hongseok Tae >> > _______________________________________________ > 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 Jul 25 00:38:25 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jul 2010 00:38:25 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 Message-ID: Hi All, Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- MAJ From david.breimann at gmail.com Sun Jul 25 08:17:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 15:17:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") Message-ID: Hi, I'm using bp_genbank2gff3.pl and seems to work fine, but when I use the -y (split) option it always gives an error on the very last line of the genbank, whch is actually "//": For example, Can't use an undefined value as a symbol reference at /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. What's the problem? Thanks, Dave From dan.bolser at gmail.com Sun Jul 25 09:23:35 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 14:23:35 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? Message-ID: Hi all, The following bug report boils down to this question: How should two sequence objects be compared for identity? Does the object override 'eq' or implement an 'identical' method? I found the following apparent bug in Contig.pm while executing the documented 'SYNOPSIS' code: #!/usr/bin/perl -w use strict; use Bio::Assembly::Contig; my $c = Bio::Assembly::Contig-> new( -id => '1' ); my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' ); my $ls_coord = Bio::SeqFeature::Generic-> new( -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); $c->set_seq_coord( $ls_coord, $ls ); Gives the following WARNINGs: --------------------- WARNING --------------------- MSG: Adding sequence r1, which has already been added --------------------------------------------------- --------------------- WARNING --------------------- MSG: Replacing one sequence [r1] --------------------------------------------------- It seems to be a bug in the documented behaviour of set_seq_coord: "If the sequence was previously added using add_seq, its coordinates are changed/set. Otherwise, add_seq is called and the sequence is added to the contig." The offending line in that function seems to be: if( ... && ($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { ... } $self->add_seq($seq); which compares the *passed* sequence object to the sequence string for the *stored* sequence object of the same name. This comparison is always fails if I understood correctly, therefore set_seq_coord always spews warnings if called after add_seq. Out of curiosity, how come I can't just say: my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); I hope the above report can be of some use. Sincerely, Dan. From robfsouza at gmail.com Sun Jul 25 10:42:35 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sun, 25 Jul 2010 10:42:35 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Hi Dan, It is been a long time since I last loooked at this but, if I remember correctly, the point is that Bio:: On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: > The following bug report boils down to this question: > How should two sequence objects be compared for identity? Does the > object override 'eq' or implement an 'identical' method? I think an 'identical' or 'equal' method would be the best alternative since having a full method call would allow passing arguments like '-mode => "complete"' to check all sequence features and annotations if they exist and '-mode => "basic"' to check id() and seq() values. Bio::Assembly::Contig depends mostly on the last one, although only id() is tracked most of the time (because of the internal hashes). > I found the following apparent bug in Contig.pm while executing the > documented 'SYNOPSIS' code: [snip] > It seems to be a bug in the documented behaviour of set_seq_coord: > ? ? ? ?"If the sequence was previously added using add_seq, its > coordinates are changed/set. ?Otherwise, add_seq is called and the > sequence is added to the contig." In fact, it should not print warnings all the time.... > The offending line in that function seems to be: > ?if( ... && > ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { > ? ? ? ? ?... > ?} > ?$self->add_seq($seq); > which compares the *passed* sequence object to the sequence string for > the *stored* sequence object of the same name. This comparison is > always fails if I understood correctly, therefore set_seq_coord always > spews warnings if called after add_seq. Not the sequence string, but the objects themselves, i.e. the string perl uses to represent Bio::LocatableSeq objects... it is a memory based version of identical() :) > Out of curiosity, how come I can't just say: > my $ls = Bio::LocatableSeq-> > ?new( -seq ? ? ?=> 'ACCG-T', > ? ? ? -id ? ? ? => 'r1', > ? ? ? -alphabet => 'dna' > ? ? ? -start ? ?=> 3, > ? ? ? -end ? ? ?=> 8, > ? ? ? -strand ? => 1 > ? ? ); > $c->add_seq( $ls ); Oh, I don't remember but it was either a bad design decision I made 8 years ago to acommodate the Bio::Align::AlignI interface or a problem with Bio::SeqFeature::Collection at that time. Whatever the case, it would be nice to change it... you just need to create a Bio::SeqFeature::Generic when add_seq is called. I just won't have time to do it myself so feel free to act... Best, Robson > I hope the above report can be of some use. > > Sincerely, > Dan. > _______________________________________________ > 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 Sun Jul 25 12:35:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:35:42 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Cheers for the clarification Robson. How come the 'SYNOPSIS' code does produce warnings about replacing the seq? (the workaround is easy enough, don't add_seq, but still...) Since you said 'feel free to act', I have been faffing around here: http://github.com/dbolser/bioperl-live I'm not really sure if that is so useful, please advise. Thanks again for help, Dan. P.S. How come you are not in irc://irc.freenode.net/#bioperl ;-) On 25 July 2010 15:42, Robson de Souza wrote: > Hi Dan, > > It is been a long time since I last loooked at this but, if I remember > correctly, the point is that Bio:: > > On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >> The following bug report boils down to this question: >> How should two sequence objects be compared for identity? Does the >> object override 'eq' or implement an 'identical' method? > > I think an 'identical' or 'equal' method would be the best alternative > since having a full method call would allow passing arguments like > '-mode => "complete"' to check all sequence features and annotations > if they exist and '-mode => "basic"' to check id() and seq() values. > Bio::Assembly::Contig depends mostly on the last one, although only > id() is tracked most of the time (because of the internal hashes). > >> I found the following apparent bug in Contig.pm while executing the >> documented 'SYNOPSIS' code: > [snip] >> It seems to be a bug in the documented behaviour of set_seq_coord: >> ? ? ? ?"If the sequence was previously added using add_seq, its >> coordinates are changed/set. ?Otherwise, add_seq is called and the >> sequence is added to the contig." > > In fact, it should not print warnings all the time.... > >> The offending line in that function seems to be: >> ?if( ... && >> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >> ? ? ? ? ?... >> ?} >> ?$self->add_seq($seq); >> which compares the *passed* sequence object to the sequence string for >> the *stored* sequence object of the same name. This comparison is >> always fails if I understood correctly, therefore set_seq_coord always >> spews warnings if called after add_seq. > > Not the sequence string, but the objects themselves, i.e. the string > perl uses to represent Bio::LocatableSeq objects... it is a memory > based version of identical() :) > >> Out of curiosity, how come I can't just say: >> my $ls = Bio::LocatableSeq-> >> ?new( -seq ? ? ?=> 'ACCG-T', >> ? ? ? -id ? ? ? => 'r1', >> ? ? ? -alphabet => 'dna' >> ? ? ? -start ? ?=> 3, >> ? ? ? -end ? ? ?=> 8, >> ? ? ? -strand ? => 1 >> ? ? ); >> $c->add_seq( $ls ); > > Oh, I don't remember but it was either a bad design decision I made 8 > years ago to acommodate the Bio::Align::AlignI interface or a problem > with Bio::SeqFeature::Collection at that time. Whatever the case, it > would be nice to change it... you just need to create a > Bio::SeqFeature::Generic when > add_seq is called. I just won't have time to do it myself so feel free to act... > > Best, > Robson > >> I hope the above report can be of some use. >> >> Sincerely, >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From dan.bolser at gmail.com Sun Jul 25 12:40:21 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:40:21 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? Message-ID: Which objects implement SeqFeatureI, and how should I find that info? Sorry for the gratuitous noobs. Cheers, Dan. From genehack at genehack.org Sun Jul 25 14:06:55 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:06:55 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> (This is in reference to: ; sorry I'm not responding to the original message but I wasn't on the list at that point.) There are really two issues being reported here. First, bp_seqfeature_gff3.PLS throws the following error when used with Bio::SeqFeature::Store::DBI::SQLite: > Can't locate object method "gff3_string" via package "Bio::SeqFeature::Generic" at /Users/jhannah/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS line 58. Second, when called on a database that's been built with '$db->no_blobs(1)', the output doesn't actually include any features. I've got a fix for the first bug in . (I've submitted a pull request for that branch to the 'bioperl' user.) Basically, when looping over the feature objects in bp_seqfeature_gff3.PLS, we introspect each one to find out if it supports the gff3_string() or gff_string() methods, and either call the appropriate one or throw an exception. (I considered just calling gff_string() instead of doing the introspection, since (a) that's the interface documented in SeqFeatureI and (b) SeqFeature::Lite, which is the only thing that currently implements gff3_string() _also_ implements gff_string(), which recalls gff3_string() when appropriate, but in the end decided that this way preserves the original intent of the script as much as possible...) I'm working on something that may be a fix for the second issue as well, but thought I'd throw this first bit out for comments, being as this is the first change I've contributed back to the project. thanks, john. From genehack at genehack.org Sun Jul 25 14:36:07 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:36:07 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> Message-ID: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> On Jul 25, 2010, at 2:06 PM, John Anderson wrote: > Second, when called on a database that's been built with '$db->no_blobs(1)', the output [ snip ] I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. (A pull request for this change has been sent to the 'bioperl' user on Github.) thanks, john. From genehack at genehack.org Sun Jul 25 14:58:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:58:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > the -y (split) option it always gives an error on the very last line > of the genbank, whch is actually "//": > > For example, > > Can't use an undefined value as a symbol reference at > /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > > What's the problem? > I filed a bug for you; it's #3124 and can be seen at The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS > index 1216810..6bdae9d 100755 > --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > @@ -654,7 +654,7 @@ for my $file ( @files ) { > } > > ## FIXME for piped output w/ split FA files ... > - close($lumpfa_fh); > + close($lumpfa_fh) if $lumpfa_fh; > if (!$split && $outfa && $lump_fh) { > print $lump_fh "##FASTA\n"; # GFF3 spec > open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > > chrs, john. From cjfields at illinois.edu Sun Jul 25 15:18:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:18:41 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> Message-ID: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> On Jul 25, 2010, at 1:36 PM, John Anderson wrote: > On Jul 25, 2010, at 2:06 PM, John Anderson wrote: >> Second, when called on a database that's been built with '$db->no_blobs(1)', the output > [ snip ] > > I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. > > I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. > > (A pull request for this change has been sent to the 'bioperl' user on Github.) > > thanks, > john. On this one (in Bio::DB::SeqFeature::DBI::mysql): if ( $typeid and $db_seqid and $start and $end and $strand ) { # then we're good... } else { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Changing this to the following should work and is more direct: if ( !defined($typeid) || !defined($db_seqid) || !defined($start) || !defined($end) || !defined($strand) ) { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Might even work shortening to a grep: if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} chris From cjfields at illinois.edu Sun Jul 25 15:20:09 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:20:09 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Pull request was merged into master branch of bioperl-live. Thanks! Oddly, pull requests aren't coming through via the mail list, I'll look into the issue. chris On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use >> the -y (split) option it always gives an error on the very last line >> of the genbank, whch is actually "//": >> >> For example, >> >> Can't use an undefined value as a symbol reference at >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. >> >> What's the problem? >> > > I filed a bug for you; it's #3124 and can be seen at > > The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> index 1216810..6bdae9d 100755 >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> @@ -654,7 +654,7 @@ for my $file ( @files ) { >> } >> >> ## FIXME for piped output w/ split FA files ... >> - close($lumpfa_fh); >> + close($lumpfa_fh) if $lumpfa_fh; >> if (!$split && $outfa && $lump_fh) { >> print $lump_fh "##FASTA\n"; # GFF3 spec >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; >> >> > > chrs, > john. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Sun Jul 25 15:48:22 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 15:48:22 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: On Jul 25, 2010, at 3:18 PM, Chris Fields wrote: > On this one (in Bio::DB::SeqFeature::DBI::mysql): > > if ( $typeid and $db_seqid and $start and $end and $strand ) { Yeah, sorry, that sort of bugged me too, but once I got into testing stuff I forgot to go back and clean it up... > Might even work shortening to a grep: > > if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} Ended up with: # if we weren't called with all the params, pull those out of the database too if ( not ( grep { defined($_) } ( ... ))) { ... } because having the negation buried inside the grep block seemed confusing... I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) j. From david.breimann at gmail.com Sun Jul 25 15:52:53 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 22:52:53 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. Thanks! On Sun, Jul 25, 2010 at 10:20 PM, Chris Fields wrote: > Pull request was merged into master branch of bioperl-live. Thanks! > > Oddly, pull requests aren't coming through via the mail list, I'll look > into the issue. > > chris > > On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > > > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > > > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > >> the -y (split) option it always gives an error on the very last line > >> of the genbank, whch is actually "//": > >> > >> For example, > >> > >> Can't use an undefined value as a symbol reference at > >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > >> > >> What's the problem? > >> > > > > I filed a bug for you; it's #3124 and can be seen at < > http://bugzilla.open-bio.org/show_bug.cgi?id=3124> > > > > The following patch fixes it for me; it can be found in < > http://github.com/genehack/bioperl-live/tree/topic/bug-3124>. I've sent a > pull request for this change. > > > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS > b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> index 1216810..6bdae9d 100755 > >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> @@ -654,7 +654,7 @@ for my $file ( @files ) { > >> } > >> > >> ## FIXME for piped output w/ split FA files ... > >> - close($lumpfa_fh); > >> + close($lumpfa_fh) if $lumpfa_fh; > >> if (!$split && $outfa && $lump_fh) { > >> print $lump_fh "##FASTA\n"; # GFF3 spec > >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > >> > >> > > > > chrs, > > john. > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From genehack at genehack.org Sun Jul 25 16:05:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 16:05:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <139B16C1-C964-4C9A-AB7F-A6566749B215@genehack.org> On Jul 25, 2010, at 3:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Or you could just change the one line in the script yourself; that was the only change. > Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Could you send me (not the list, just me) an input file that produces this problem? > Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. It looks like the '-n' option should do that, but it currently throws a few more errors of the same general type as you were seeing before -- let me look at those... j. From David.Messina at sbc.su.se Sun Jul 25 16:34:42 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 25 Jul 2010 14:34:42 -0600 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> On Jul 25, 2010, at 13:48, John Anderson wrote: > > I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) You've probably seen this, right? http://www.bioperl.org/wiki/Bioperl_Best_Practices Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) Thanks for all your work on this, John! Dave From biopython at maubp.freeserve.co.uk Sun Jul 25 17:10:30 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 25 Jul 2010 22:10:30 +0100 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: On Sun, Jul 25, 2010 at 8:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view > to use to updated version should I first update my clone of bioperl-live > (git pull?) then go through the whole build and install again? > > Second, I have just noticed that bp_genbank2gff3.pl returns an error when > given a circular genome with a feature that spans the "end" of the genome > (e.g., assume the genome size is 1000np and a feature spans > join(900..1000,1..100). The GFF3 spec has recently been updated to cover circular genomes explicitly - this script probably needs updating in light of this. Peter From hlapp at drycafe.net Sun Jul 25 17:26:39 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 25 Jul 2010 17:26:39 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: Message-ID: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > Hi All, > Our BP poster from the conference is available on SlideShare (search > BioPerl ISMB 2010) and on my wiki homepage. Enjoy- If anyone was wondering about the URL: http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 Mark - were you going to post a news item on this? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sun Jul 25 19:05:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:05:49 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> Message-ID: <9F8B93B0-40B4-4D36-AFC8-42AB0F640E80@illinois.edu> On Jul 25, 2010, at 3:34 PM, Dave Messina wrote: > On Jul 25, 2010, at 13:48, John Anderson wrote: >> >> I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) > > You've probably seen this, right? > > http://www.bioperl.org/wiki/Bioperl_Best_Practices > > Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) > > Thanks for all your work on this, John! > > > > Dave Agreed, thanks John. I'll pull this into a local branch and test, then pull in if everything's okay. chris From cjfields at illinois.edu Sun Jul 25 19:09:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:22 -0500 Subject: [Bioperl-l] BOSC 2010 BioPerl slides Message-ID: <94B38B72-EC74-49AA-B8E6-7E0E0ABDEBFA@illinois.edu> Just a note that, along with Mark's poster, I gave a smallish update on BioPerl at BOSC 2010: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Feedback welcome! chris From cjfields at illinois.edu Sun Jul 25 19:09:35 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:35 -0500 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> Message-ID: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > > On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >> Hi All, >> Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > > If anyone was wondering about the URL: > > http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > > Mark - were you going to post a news item on this? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== We could do this along with posting the slides for the BOSC BioPerl talk: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl chris From cjfields at illinois.edu Sun Jul 25 19:11:06 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:11:06 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <9FB52BF8-532C-4FA2-A590-4ECDA9700E8B@illinois.edu> On Jul 25, 2010, at 4:10 PM, Peter wrote: > On Sun, Jul 25, 2010 at 8:52 PM, David Breimann > wrote: >> Thank you guys. I'm quite new to all this github stuff, so in order to view >> to use to updated version should I first update my clone of bioperl-live >> (git pull?) then go through the whole build and install again? >> >> Second, I have just noticed that bp_genbank2gff3.pl returns an error when >> given a circular genome with a feature that spans the "end" of the genome >> (e.g., assume the genome size is 1000np and a feature spans >> join(900..1000,1..100). > > The GFF3 spec has recently been updated to cover circular > genomes explicitly - this script probably needs updating in light > of this. > > Peter We need to add a few tests for circular genomes with BioPerl; I'm pretty sure these currently do not work as expected. chris From grapevine.256 at gmail.com Mon Jul 26 00:27:16 2010 From: grapevine.256 at gmail.com (Vidya Oruganti) Date: Mon, 26 Jul 2010 12:27:16 +0800 Subject: [Bioperl-l] Restriction Analysis Message-ID: Dear All, I am interested in knowing if there is a way to perform the restriction analysis module on many sequences at once. Currently I am retrieving sequences of contigs one by one from genbank and performing the restriction analysis individually. This is the script I am using: use Bio::Restriction::Analysis; use Bio::DB::GenBank; use Data::Dumper; use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); $seq = $gb->get_Seq_by_gi('405830'); # GI Number my $ra = Bio::Restriction::Analysis->new(-seq=>$seq); print "There are ", scalar $ra->zero_cutters->each_enzyme, " enzymes that do not cut\n"; printf "\n%-10s%s\n", 'Enzyme', 'Number of Cuts'; my $all_cutters = $ra->cutters; map { printf "%-10s%s\n", $_->name, $ra->cuts_by_enzyme($_->name) } $all_cutters->each_enzyme; I would like to know whether it would be possible to get an array of sequences from genbank instead of just one and run the restriction analysis on all the sequences at one go and get several outputs at once. I have been able to retrieve more than one sequence from genbank but I'm not able to run the analysis on more than one sequence. Thank you From adsj at novozymes.com Mon Jul 26 03:09:54 2010 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 26 Jul 2010 09:09:54 +0200 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> (Chris Fields's message of "Sun, 25 Jul 2010 18:09:35 -0500") References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> Message-ID: <87eieqen25.fsf@topper.koldfront.dk> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> Our BP poster from the conference is available on SlideShare (search >>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Any chance of posting these slides for download somewhere that doesn't require creating an account to do so? Best wishes, Adam, just curious. -- Adam Sj?gren adsj at novozymes.com From avilella at gmail.com Mon Jul 26 05:08:32 2010 From: avilella at gmail.com (Albert Vilella) Date: Mon, 26 Jul 2010 10:08:32 +0100 Subject: [Bioperl-l] Run wrappers for BWA and Samtools In-Reply-To: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> References: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> Message-ID: Hi Mark, First of all, great work. Can I ask if the aim of combining bwa and samtools would be or could be to replicate "maq.pl easyrun" ? Or what would be an alternative for users wanting to do "maq.pl easyrun" for a combination of long and short reads? Cheers, Albert. On Sat, Nov 28, 2009 at 5:23 PM, Mark A. Jensen wrote: > Hi All, > > Run wrappers for the bwa assembler and the samtools suite > are now available as beta in the bioperl-run/trunk. The bwa > wrapper allows you to run a canned assembly pipeline, or > to execute individual bwa components. The assembly pipeline > can return a Bio::Assembly::Scaffold object via the new > Bio::Assembly::IO::sam module in bioperl-live/trunk > (this requires lstein's Bio::DB::Sam, from CPAN). Details at > > http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA > > and, of course, in the pod. > > Cheers, > MAJ > _______________________________________________ > 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 Jul 26 09:38:01 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:38:01 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 Message-ID: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.com > > _______________________________________________ > 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 Jul 26 09:18:56 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:18:56 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Hi Benard, Forwarding to the list for more help for you. You may want to look at the POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to use this module to create an OrthoMCL wrapper. This might be more technical than you want. Maybe a dev on the list would be interested in creating a wrapper using CommandExts. cheers, MAJ ----- Original Message ----- From: "Benard Kulohoma" To: Sent: Wednesday, July 21, 2010 10:58 AM Subject: Inquiry Hi Mark, I just read your bioperl resource on BWA (and here: http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was most helpful. Do you have any idea of how I could use Bioperl to implement OrthoMCL of several bacterial genomes. I would like to find some membrane proteins. Many thanks, Benard PS: I am sorry for spaming/inquiring!! :) -- 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 roy.chaudhuri at gmail.com Mon Jul 26 09:46:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 26 Jul 2010 14:46:49 +0100 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: <4C4D91C9.4090704@gmail.com> Thanks for this Mark. Just in case anyone can't find it, it's here: http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png Roy. On 26/07/2010 14:38, Mark A. Jensen wrote: > missed the list-- > ----- Original Message ----- > From: "Mark A. Jensen" > To: "Adam "Sj?gren"" > Sent: Monday, July 26, 2010 9:37 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > >> There's a png version of the poster on my wiki page >> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >> wiki thinks it should?). Chris, maybe could upload yours to wiki? >> cheers MAJ >> ----- Original Message ----- >> From: "Adam "Sj?gren"" >> To: >> Sent: Monday, July 26, 2010 3:09 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >> >>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> >>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >> >>>>> Our BP poster from the conference is available on SlideShare (search >>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> >>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >> >>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >> >> Any chance of posting these slides for download somewhere that doesn't >> require creating an account to do so? >> >> >> Best wishes, >> >> Adam, just curious. >> >> -- >> Adam Sj?gren >> adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 09:46:38 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:46:38 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: http://bioperl.org/wiki/Mark_Jensen, it is... ----- Original Message ----- From: "Mark A. Jensen" To: "BioPerl List" Sent: Monday, July 26, 2010 9:38 AM Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 10:05:12 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 10:05:12 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4C4D91C9.4090704@gmail.com> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: http://posters.f1000.com/PosterList?posterID=246 ----- Original Message ----- From: "Roy Chaudhuri" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, July 26, 2010 9:46 AM Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > Thanks for this Mark. Just in case anyone can't find it, it's here: > http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png > > Roy. > > On 26/07/2010 14:38, Mark A. Jensen wrote: >> missed the list-- >> ----- Original Message ----- >> From: "Mark A. Jensen" >> To: "Adam "Sj?gren"" >> Sent: Monday, July 26, 2010 9:37 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >>> There's a png version of the poster on my wiki page >>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with >>> uploading >>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>> cheers MAJ >>> ----- Original Message ----- >>> From: "Adam "Sj?gren"" >>> To: >>> Sent: Monday, July 26, 2010 3:09 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>> >>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>> >>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> >>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>> >>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>> >>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>> >>> Any chance of posting these slides for download somewhere that doesn't >>> require creating an account to do so? >>> >>> >>> Best wishes, >>> >>> Adam, just curious. >>> >>> -- >>> Adam Sj?gren >>> adsj at novozymes.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 amackey at virginia.edu Mon Jul 26 10:51:43 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Mon, 26 Jul 2010 10:51:43 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes sense to "wrap" it. See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt -Aaron On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > Hi Benard, > Forwarding to the list for more help for you. You may want to look at the > POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live > distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to > use this module to create an OrthoMCL wrapper. This might be more technical > than you want. Maybe a dev on the list would be interested in creating a > wrapper using CommandExts. > cheers, MAJ > ----- Original Message ----- From: "Benard Kulohoma" < > B.Kulohoma at liverpool.ac.uk> > To: > Sent: Wednesday, July 21, 2010 10:58 AM > Subject: Inquiry > > > Hi Mark, > > I just read your bioperl resource on BWA (and here: > http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was > most helpful. Do you have any idea of how I could use Bioperl to implement > OrthoMCL of several bacterial genomes. I would like to find some membrane > proteins. > > Many thanks, > > Benard > > PS: I am sorry for spaming/inquiring!! :) > > -- > 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. > > > _______________________________________________ > 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 Jul 26 11:05:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 10:05:05 -0500 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: <84B78CA5-5D0E-447C-B507-8FCA18EDA7CB@illinois.edu> Agreed; I'm using it locally. I could see subclassing BLAST (or similar) wrappers specifically for the all-v-all portion of the pipeline (for consistency/flexibility), but I get along w/o that. chris On Jul 26, 2010, at 9:51 AM, Aaron Mackey wrote: > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 maj at fortinbras.us Mon Jul 26 11:07:35 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 11:07:35 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Maybe not in the sense of CommandExts, but a BioPerl module that does the "13 steps" might be very useful. (Not saying anyone should do it :) ) ----- Original Message ----- From: "Aaron Mackey" To: "Mark A. Jensen" Cc: "BioPerl List" ; "Benard Kulohoma" Sent: Monday, July 26, 2010 10:51 AM Subject: Re: [Bioperl-l] Inquiry on OrthoMCL > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Jul 26 11:35:18 2010 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jul 2010 11:35:18 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, I think there are probably several BioPerl classes that implement Bio::SeqFeatureI, like Bio::SeqFeature::Generic. What are you looking for? Scott On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: > Which objects implement SeqFeatureI, and how should I find that info? > > Sorry for the gratuitous noobs. > > Cheers, > Dan. > _______________________________________________ > 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 Mon Jul 26 12:22:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 11:22:54 -0500 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: I've added the PDF version of the BOSC 2010 talk and both the PDF and .ppt versions of the ISMB 2010 BioPerl poster here: http://www.bioperl.org/DIST/presentations/ Just a warning, the PDF of the poster has copyright notices all over it (I'll post a clean one if it's emailed to me!). Mark, did you want to make a blog post about these? chris On Jul 26, 2010, at 9:05 AM, Mark A. Jensen wrote: > Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: > http://posters.f1000.com/PosterList?posterID=246 > ----- Original Message ----- From: "Roy Chaudhuri" > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Monday, July 26, 2010 9:46 AM > Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > > >> Thanks for this Mark. Just in case anyone can't find it, it's here: >> http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png >> >> Roy. >> >> On 26/07/2010 14:38, Mark A. Jensen wrote: >>> missed the list-- >>> ----- Original Message ----- >>> From: "Mark A. Jensen" >>> To: "Adam "Sj?gren"" >>> Sent: Monday, July 26, 2010 9:37 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>>> There's a png version of the poster on my wiki page >>>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >>>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>>> cheers MAJ >>>> ----- Original Message ----- >>>> From: "Adam "Sj?gren"" >>>> To: >>>> Sent: Monday, July 26, 2010 3:09 AM >>>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>>> >>>> >>>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>>> >>>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>>> >>>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>>> >>>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>>> >>>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>>> >>>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>>> >>>> Any chance of posting these slides for download somewhere that doesn't >>>> require creating an account to do so? >>>> >>>> >>>> Best wishes, >>>> >>>> Adam, just curious. >>>> >>>> -- >>>> Adam Sj?gren >>>> adsj at novozymes.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 >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Mon Jul 26 13:54:22 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Mon, 26 Jul 2010 13:54:22 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: > Thanks again Robson, > > One thing I was going to email the list about is a lack of tests for > ace.pm and phrap.pm ... because of missing libs I'm not running the > sam or the maq tests, so any changes that I'm making to Contig.pm / > Scaffold.pm are not really being tested. > > Do you think anyone on the list (or you) would be able to generate a > few hundred tests to help me start modifying code with confidence? I hope so. I was reading Chris's presentation at BOSC and he mentioned that people are working on the support for the samtools so I believe somebody must have a dataset they could share. > One idea was to actually make Contig.pm implement SeqFeatureI, so that > you could call start and end and seq on the contig (consensus) > directly. > > Here are some notes from IRC... > > 04:00 < dbolser> I think "$contig_object->start" is totally reasonable > 04:01 < dbolser> otherwise its something like > "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" > 04:02 < dbolser> (untested ;-) > 09:01 < genehack> dbolser: i think you've got an argument that there should be; > it's probably going to be a lot easier to do that in > something like Biome (i.e., BioPerl in Moose) Never thought about it... but I can see that could be useful when contigs are part of higher level assemblies, like scaffolds or assembled chromosomes, but you could also achieve this by making Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any reason to prefer the Bio::SeqFeatureI interface? > Any reason not to cc this to the list? Lack of attention. I was so concerned about the answer that I didn't notice I pressed "Reply to" :) Best, Robson > Thanks again. > > All the best, > Dan. > > > > > On 26 July 2010 17:23, Robson de Souza wrote: >> Hi, >> >> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>> Cheers for the clarification Robson. >> >> You are welcome :). Thanks for improving my long abandoned child... :) >> >>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>> seq? (the workaround is easy enough, don't add_seq, but still...) >> >> I don't know. I remember testing it while I develop Contig.pm in >> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >> Did you try ace.pm recently? It uses set_seq_coord and this method >> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >> of previous bug reports on ace.pm regarding unexpected warnings... >> note that set_seq_coord calls remove_seq before adding but prints >> another warning. Compare set_seq_coord to add_seq alone and maybe you >> will figure out what is going on... >> >> Regarding why you can't just add Bio::LocatableSeq objects and have >> add_seq just set the coordinates by itself, I investigated my long >> forgotten code and just realized that the whole problem was that the >> coordinates of a Bio::LocatableSeq object represent the location of >> the object in the original sequence (i.e. unaligned read coordinates) >> instead of its coordinates in the aligned consensus sequence. >> Bio::LocatableSeq issues a warning whenever you try to set the object >> start and end coordinates to the gapped consensus coordinates because >> such coordinates lead to a length shorter than the actual read length: >> >> use Bio::LocatableSeq; >> use Bio::SeqFeature::Collection; >> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >> =>"agggcACT-Gccc", -id=>"uga"); >> my $sfc = Bio::SeqFeature::Collection->new(); >> $sfc->add_features([ $ls ]); >> print $sfc->feature_count,"\t",$ls->length."\n"; >> >> Additionally, Bio::LocatableSeq objects do not support the >> primary_tag() method because they are just Bio::RangeI and not >> Bio::SeqFeatureI objects. These two issues prevented me from using >> Bio::LocatableSeq coordinates to represent gapped consensus >> coordinates but the example code above suggests suppressing >> Bio::LocatableSeq warnings and using the object class >> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >> the need for extra Bio::SeqFeature::Generic objects to store read >> coordinates. >> >>> Since you said 'feel free to act', I have been faffing around here: >>> http://github.com/dbolser/bioperl-live >>> I'm not really sure if that is so useful, please advise. >> >> The comments I made above points to one area where you could have some >> improvements in both memory usage and usability: drop the need for >> additional Bio::SeqFeatureI objects to represent gapped consensus >> coordinates. It would require you to check all Contig.pm methods for >> the use of the "_aligned_coord:$readID" tags (I don't expect to see >> any references to this outside Contig.pm) and change set_seq_coord to >> a method that changes/sets the start and end values of the >> Bio::LocatableSeq objects. >> This might be a bit of work so just go for it if you want and have >> time to experiment. >> >> Another detail: could you please replace references in Contig.pm and >> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >> not exists to the correct Bio::* classes? Somebody changed this to the >> wrong names long ago... >> >>> Thanks again for help, >> >> Well these are my thoughts on the matter. Write again if you decide to >> take this on and are unable to make progress. >> Best, >> Robson >> >>> Dan. >>> >>> >>> P.S. >>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>> >>> >>> On 25 July 2010 15:42, Robson de Souza wrote: >>>> Hi Dan, >>>> >>>> It is been a long time since I last loooked at this but, if I remember >>>> correctly, the point is that Bio:: >>>> >>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>> The following bug report boils down to this question: >>>>> How should two sequence objects be compared for identity? Does the >>>>> object override 'eq' or implement an 'identical' method? >>>> >>>> I think an 'identical' or 'equal' method would be the best alternative >>>> since having a full method call would allow passing arguments like >>>> '-mode => "complete"' to check all sequence features and annotations >>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>> id() is tracked most of the time (because of the internal hashes). >>>> >>>>> I found the following apparent bug in Contig.pm while executing the >>>>> documented 'SYNOPSIS' code: >>>> [snip] >>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>> sequence is added to the contig." >>>> >>>> In fact, it should not print warnings all the time.... >>>> >>>>> The offending line in that function seems to be: >>>>> ?if( ... && >>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>> ? ? ? ? ?... >>>>> ?} >>>>> ?$self->add_seq($seq); >>>>> which compares the *passed* sequence object to the sequence string for >>>>> the *stored* sequence object of the same name. This comparison is >>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>> spews warnings if called after add_seq. >>>> >>>> Not the sequence string, but the objects themselves, i.e. the string >>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>> based version of identical() :) >>>> >>>>> Out of curiosity, how come I can't just say: >>>>> my $ls = Bio::LocatableSeq-> >>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>> ? ? ? -id ? ? ? => 'r1', >>>>> ? ? ? -alphabet => 'dna' >>>>> ? ? ? -start ? ?=> 3, >>>>> ? ? ? -end ? ? ?=> 8, >>>>> ? ? ? -strand ? => 1 >>>>> ? ? ); >>>>> $c->add_seq( $ls ); >>>> >>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>> would be nice to change it... you just need to create a >>>> Bio::SeqFeature::Generic when >>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>> >>>> Best, >>>> Robson >>>> >>>>> I hope the above report can be of some use. >>>>> >>>>> Sincerely, >>>>> Dan. >>>>> _______________________________________________ >>>>> 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 Tue Jul 27 04:53:49 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 09:53:49 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 26 July 2010 16:35, Scott Cain wrote: > Hi Dan, > > I think there are probably several BioPerl classes that implement > Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking > for? A way to find what implements what... something like javadoc for bp. Really I'm looking for a nice 'ontology' of SeqFeatures. I was thinking that Contig.pm should implement Bio::SeqFeatureI. > Scott > > > On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >> Which objects implement SeqFeatureI, and how should I find that info? >> >> Sorry for the gratuitous noobs. >> >> Cheers, >> Dan. >> _______________________________________________ >> 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 dan.bolser at gmail.com Tue Jul 27 05:02:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 10:02:05 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On 26 July 2010 18:54, Robson de Souza wrote: > On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >> Thanks again Robson, >> >> One thing I was going to email the list about is a lack of tests for >> ace.pm and phrap.pm ... because of missing libs I'm not running the >> sam or the maq tests, so any changes that I'm making to Contig.pm / >> Scaffold.pm are not really being tested. >> >> Do you think anyone on the list (or you) would be able to generate a >> few hundred tests to help me start modifying code with confidence? > > I hope so. I was reading Chris's presentation at BOSC and he mentioned > that people are working on the support for the samtools so I believe > somebody must have a dataset they could share. Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because I don't have samtools installed. Also, (quick impression) method coverage is limited (Contig.pm has a lot of methods!). I'll try to write some tests for ace.pm and phrap.pm. >> One idea was to actually make Contig.pm implement SeqFeatureI, so that >> you could call start and end and seq on the contig (consensus) >> directly. >> >> Here are some notes from IRC... >> >> 04:00 < dbolser> I think "$contig_object->start" is totally reasonable >> 04:01 < dbolser> otherwise its something like >> "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" >> 04:02 < dbolser> (untested ;-) >> 09:01 < genehack> dbolser: i think you've got an argument that there should be; >> ? ? ? ? ? ? ? ? ?it's probably going to be a lot easier to do that in >> ? ? ? ? ? ? ? ? ?something like Biome (i.e., BioPerl in Moose) > > Never thought about it... but I can see that could be useful when > contigs are part of higher level assemblies, like scaffolds or > assembled chromosomes, but you could also achieve this by making > Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any > reason to prefer the Bio::SeqFeatureI interface? No. I don't have an overview of how the various objects relate to one another, so any choice is more or less arbitrary. I'll try to write a 'Sequence HOWTO'. Thanks again for help, Dan. >> Any reason not to cc this to the list? > > Lack of attention. I was so concerned about the answer that I didn't > notice I pressed "Reply to" :) > Best, > Robson > >> Thanks again. >> >> All the best, >> Dan. >> >> >> >> >> On 26 July 2010 17:23, Robson de Souza wrote: >>> Hi, >>> >>> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>>> Cheers for the clarification Robson. >>> >>> You are welcome :). Thanks for improving my long abandoned child... :) >>> >>>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>>> seq? (the workaround is easy enough, don't add_seq, but still...) >>> >>> I don't know. I remember testing it while I develop Contig.pm in >>> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >>> Did you try ace.pm recently? It uses set_seq_coord and this method >>> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >>> of previous bug reports on ace.pm regarding unexpected warnings... >>> note that set_seq_coord calls remove_seq before adding but prints >>> another warning. Compare set_seq_coord to add_seq alone and maybe you >>> will figure out what is going on... >>> >>> Regarding why you can't just add Bio::LocatableSeq objects and have >>> add_seq just set the coordinates by itself, I investigated my long >>> forgotten code and just realized that the whole problem was that the >>> coordinates of a Bio::LocatableSeq object represent the location of >>> the object in the original sequence (i.e. unaligned read coordinates) >>> instead of its coordinates in the aligned consensus sequence. >>> Bio::LocatableSeq issues a warning whenever you try to set the object >>> start and end coordinates to the gapped consensus coordinates because >>> such coordinates lead to a length shorter than the actual read length: >>> >>> use Bio::LocatableSeq; >>> use Bio::SeqFeature::Collection; >>> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >>> =>"agggcACT-Gccc", -id=>"uga"); >>> my $sfc = Bio::SeqFeature::Collection->new(); >>> $sfc->add_features([ $ls ]); >>> print $sfc->feature_count,"\t",$ls->length."\n"; >>> >>> Additionally, Bio::LocatableSeq objects do not support the >>> primary_tag() method because they are just Bio::RangeI and not >>> Bio::SeqFeatureI objects. These two issues prevented me from using >>> Bio::LocatableSeq coordinates to represent gapped consensus >>> coordinates but the example code above suggests suppressing >>> Bio::LocatableSeq warnings and using the object class >>> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >>> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >>> the need for extra Bio::SeqFeature::Generic objects to store read >>> coordinates. >>> >>>> Since you said 'feel free to act', I have been faffing around here: >>>> http://github.com/dbolser/bioperl-live >>>> I'm not really sure if that is so useful, please advise. >>> >>> The comments I made above points to one area where you could have some >>> improvements in both memory usage and usability: drop the need for >>> additional Bio::SeqFeatureI objects to represent gapped consensus >>> coordinates. It would require you to check all Contig.pm methods for >>> the use of the "_aligned_coord:$readID" tags (I don't expect to see >>> any references to this outside Contig.pm) and change set_seq_coord to >>> a method that changes/sets the start and end values of the >>> Bio::LocatableSeq objects. >>> This might be a bit of work so just go for it if you want and have >>> time to experiment. >>> >>> Another detail: could you please replace references in Contig.pm and >>> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >>> not exists to the correct Bio::* classes? Somebody changed this to the >>> wrong names long ago... >>> >>>> Thanks again for help, >>> >>> Well these are my thoughts on the matter. Write again if you decide to >>> take this on and are unable to make progress. >>> Best, >>> Robson >>> >>>> Dan. >>>> >>>> >>>> P.S. >>>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>>> >>>> >>>> On 25 July 2010 15:42, Robson de Souza wrote: >>>>> Hi Dan, >>>>> >>>>> It is been a long time since I last loooked at this but, if I remember >>>>> correctly, the point is that Bio:: >>>>> >>>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>>> The following bug report boils down to this question: >>>>>> How should two sequence objects be compared for identity? Does the >>>>>> object override 'eq' or implement an 'identical' method? >>>>> >>>>> I think an 'identical' or 'equal' method would be the best alternative >>>>> since having a full method call would allow passing arguments like >>>>> '-mode => "complete"' to check all sequence features and annotations >>>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>>> id() is tracked most of the time (because of the internal hashes). >>>>> >>>>>> I found the following apparent bug in Contig.pm while executing the >>>>>> documented 'SYNOPSIS' code: >>>>> [snip] >>>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>>> sequence is added to the contig." >>>>> >>>>> In fact, it should not print warnings all the time.... >>>>> >>>>>> The offending line in that function seems to be: >>>>>> ?if( ... && >>>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>>> ? ? ? ? ?... >>>>>> ?} >>>>>> ?$self->add_seq($seq); >>>>>> which compares the *passed* sequence object to the sequence string for >>>>>> the *stored* sequence object of the same name. This comparison is >>>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>>> spews warnings if called after add_seq. >>>>> >>>>> Not the sequence string, but the objects themselves, i.e. the string >>>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>>> based version of identical() :) >>>>> >>>>>> Out of curiosity, how come I can't just say: >>>>>> my $ls = Bio::LocatableSeq-> >>>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>>> ? ? ? -id ? ? ? => 'r1', >>>>>> ? ? ? -alphabet => 'dna' >>>>>> ? ? ? -start ? ?=> 3, >>>>>> ? ? ? -end ? ? ?=> 8, >>>>>> ? ? ? -strand ? => 1 >>>>>> ? ? ); >>>>>> $c->add_seq( $ls ); >>>>> >>>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>>> would be nice to change it... you just need to create a >>>>> Bio::SeqFeature::Generic when >>>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>>> >>>>> Best, >>>>> Robson >>>>> >>>>>> I hope the above report can be of some use. >>>>>> >>>>>> Sincerely, >>>>>> Dan. >>>>>> _______________________________________________ >>>>>> 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 Jul 27 09:45:25 2010 From: scott at scottcain.net (Scott Cain) Date: Tue, 27 Jul 2010 09:45:25 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, You might find the deobfuscator helpful: http://bioperl.org/cgi-bin/deob_interface.cgi Scott On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: > On 26 July 2010 16:35, Scott Cain wrote: >> Hi Dan, >> >> I think there are probably several BioPerl classes that implement >> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >> for? > > A way to find what implements what... something like javadoc for bp. > > Really I'm looking for a nice 'ontology' of SeqFeatures. > > I was thinking that Contig.pm should implement Bio::SeqFeatureI. > > >> Scott >> >> >> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>> Which objects implement SeqFeatureI, and how should I find that info? >>> >>> Sorry for the gratuitous noobs. >>> >>> Cheers, >>> Dan. >>> _______________________________________________ >>> 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 >> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 Ontario Institute for Cancer Research From twaddlac at gmail.com Tue Jul 27 10:10:30 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:10:30 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: Hello, I am curious as to how I am supposed to use SeqIO::fastq to read in a fastq file and then obtain the nucleotide sequence from that. I noticed that SeqIO::fastq returns a Seq::Quality object but I haven't seen a method within that module that returns the nucleotide sequence. Please, let me know if you have any suggestions! Thank you very much!! -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 10:16:27 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:16:27 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: Message-ID: <4C4EEA3B.6020803@gmail.com> Hi Alan, Another case for the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say $seqqual->seq to get the sequence as a string. Cheers. Roy. On 27/07/2010 15:10, Alan Twaddle wrote: > Hello, > > I am curious as to how I am supposed to use SeqIO::fastq to read > in a fastq file and then obtain the nucleotide sequence from that. I > noticed that SeqIO::fastq returns a Seq::Quality object but I haven't > seen a method within that module that returns the nucleotide sequence. > Please, let me know if you have any suggestions! > > Thank you very much!! > From cjfields at illinois.edu Tue Jul 27 10:34:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 09:34:54 -0500 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Jul 27, 2010, at 4:02 AM, Dan Bolser wrote: > On 26 July 2010 18:54, Robson de Souza wrote: >> On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >>> Thanks again Robson, >>> >>> One thing I was going to email the list about is a lack of tests for >>> ace.pm and phrap.pm ... because of missing libs I'm not running the >>> sam or the maq tests, so any changes that I'm making to Contig.pm / >>> Scaffold.pm are not really being tested. >>> >>> Do you think anyone on the list (or you) would be able to generate a >>> few hundred tests to help me start modifying code with confidence? >> >> I hope so. I was reading Chris's presentation at BOSC and he mentioned >> that people are working on the support for the samtools so I believe >> somebody must have a dataset they could share. > > Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because > I don't have samtools installed. Also, (quick impression) method > coverage is limited (Contig.pm has a lot of methods!). > > I'll try to write some tests for ace.pm and phrap.pm. Tests are good! >> Never thought about it... but I can see that could be useful when >> contigs are part of higher level assemblies, like scaffolds or >> assembled chromosomes, but you could also achieve this by making >> Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any >> reason to prefer the Bio::SeqFeatureI interface? > > No. I don't have an overview of how the various objects relate to one > another, so any choice is more or less arbitrary. I'll try to write a > 'Sequence HOWTO'. > > > Thanks again for help, > Dan. Dan, The current HOWTOs (Beginner's, Feature/Annotation) should have this information, along with the BioPerl tutorial. chris From twaddlac at gmail.com Tue Jul 27 10:38:09 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:38:09 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EEA3B.6020803@gmail.com> References: <4C4EEA3B.6020803@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: > Hi Alan, > > Another case for the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi > > A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say > $seqqual->seq to get the sequence as a string. > > Cheers. > Roy. > > On 27/07/2010 15:10, Alan Twaddle wrote: >> >> Hello, >> >> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >> in a fastq file and then obtain the nucleotide sequence from that. I >> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >> seen a method within that module that returns the nucleotide sequence. >> Please, let me know if you have any suggestions! >> >> Thank you very much!! >> > > -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 10:50:21 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:50:21 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> Message-ID: <4C4EF22D.6050705@gmail.com> Hi Alan, It sounds like there's a problem with reading in your Fastq file. Are you using the latest BioPerl version? There have been many bug fixes to Bio::SeqIO::fastq over the last couple of years. If you are using an up-to-date BioPerl, please could you send an example Fastq entry which gives the error messages? Roy. On 27/07/2010 15:37, Alan Twaddle wrote: > Whenever I try to access the sequence I get the following error message: > > > --------------------- WARNING --------------------- > MSG: Seq/Qual descriptions don't match; using sequence description > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Fastq sequence/quality data length mismatch error > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + > --------------------------------------------------- > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Attempting to set the sequence to > [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] > which does not look healthy > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 > STACK: Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 > STACK: Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 > STACK: Bio::LocatableSeq::new > /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 > STACK: Bio::Seq::Meta::Array::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 > STACK: Bio::Seq::Quality::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 > STACK: Bio::Seq::SeqFactory::create > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 > STACK: Bio::SeqIO::fastq::next_seq > /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 > STACK: fastQParser.pl:12 > > > > On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> Another case for the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi >> >> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >> $seqqual->seq to get the sequence as a string. >> >> Cheers. >> Roy. >> >> On 27/07/2010 15:10, Alan Twaddle wrote: >>> >>> Hello, >>> >>> I am curious as to how I am supposed to use SeqIO::fastq to read >>> in a fastq file and then obtain the nucleotide sequence from that. I >>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>> seen a method within that module that returns the nucleotide sequence. >>> Please, let me know if you have any suggestions! >>> >>> Thank you very much!! >>> >> >> > > > From twaddlac at gmail.com Tue Jul 27 10:55:58 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:55:58 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EF22D.6050705@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: I'm not certain that I'm using the latest BioPerl, but I can check. In the mean time, I'll send you the example data! @FQ4HLCS02EO12Q region=2 tag=H +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII @FQ4HLCS02EO12T region=2 tag=B +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: > Hi Alan, > > It sounds like there's a problem with reading in your Fastq file. Are you > using the latest BioPerl version? There have been many bug fixes to > Bio::SeqIO::fastq over the last couple of years. If you are using an > up-to-date BioPerl, please could you send an example Fastq entry which gives > the error messages? > > Roy. > > On 27/07/2010 15:37, Alan Twaddle wrote: >> >> Whenever I try to access the sequence I get the following error message: >> >> >> --------------------- WARNING --------------------- >> MSG: Seq/Qual descriptions don't match; using sequence description >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: Fastq sequence/quality data length mismatch error >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >> --------------------------------------------------- >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Attempting to set the sequence to >> >> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >> which does not look healthy >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >> STACK: Bio::PrimarySeq::seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >> STACK: Bio::PrimarySeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >> STACK: Bio::LocatableSeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >> STACK: Bio::Seq::Meta::Array::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >> STACK: Bio::Seq::Quality::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >> STACK: Bio::Seq::SeqFactory::create >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >> STACK: Bio::SeqIO::fastq::next_seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >> STACK: fastQParser.pl:12 >> >> >> >> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >> ?wrote: >>> >>> Hi Alan, >>> >>> Another case for the deobfuscator: >>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>> $seqqual->seq to get the sequence as a string. >>> >>> Cheers. >>> Roy. >>> >>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>> >>>> Hello, >>>> >>>> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>> seen a method within that module that returns the nucleotide sequence. >>>> Please, let me know if you have any suggestions! >>>> >>>> Thank you very much!! >>>> >>> >>> >> >> >> > > -- Alan Twaddle, B.S. MUC class of 2010 From biopython at maubp.freeserve.co.uk Tue Jul 27 11:34:11 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Jul 2010 16:34:11 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > Hopefully this is just an email problem, but that doesn't look like a well formatted FASTQ record to me. Where is the "+" line separating the sequence and qualities? Maybe sending this single record as an attachment would work better (is that encouraged on this mailing list?). Peter From roy.chaudhuri at gmail.com Tue Jul 27 11:35:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 16:35:49 +0100 Subject: [Bioperl-l] Fwd: Re: How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: <4C4EFCD5.3030809@gmail.com> Forgot to cc the list: -------- Original Message -------- Subject: Re: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Date: Tue, 27 Jul 2010 16:03:53 +0100 From: Roy Chaudhuri To: Alan Twaddle That doesn't look like Fastq format as defined here: http://nar.oxfordjournals.org/cgi/content/full/gkp1137v1 http://en.wikipedia.org/wiki/FASTQ_format It shouldn't be difficult to write a script to parse it or convert to standard Fastq, though. > p.s. how do I find out what version of bioperl I'm using? http://www.bioperl.org/wiki/FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F On 27/07/2010 15:55, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > > > On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> It sounds like there's a problem with reading in your Fastq file. Are you >> using the latest BioPerl version? There have been many bug fixes to >> Bio::SeqIO::fastq over the last couple of years. If you are using an >> up-to-date BioPerl, please could you send an example Fastq entry which gives >> the error messages? >> >> Roy. >> >> On 27/07/2010 15:37, Alan Twaddle wrote: >>> >>> Whenever I try to access the sequence I get the following error message: >>> >>> >>> --------------------- WARNING --------------------- >>> MSG: Seq/Qual descriptions don't match; using sequence description >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: Fastq sequence/quality data length mismatch error >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >>> --------------------------------------------------- >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Attempting to set the sequence to >>> >>> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >>> which does not look healthy >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >>> STACK: Bio::PrimarySeq::seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >>> STACK: Bio::PrimarySeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >>> STACK: Bio::LocatableSeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >>> STACK: Bio::Seq::Meta::Array::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >>> STACK: Bio::Seq::Quality::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >>> STACK: Bio::Seq::SeqFactory::create >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >>> STACK: Bio::SeqIO::fastq::next_seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >>> STACK: fastQParser.pl:12 >>> >>> >>> >>> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >>> wrote: >>>> >>>> Hi Alan, >>>> >>>> Another case for the deobfuscator: >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>>> $seqqual->seq to get the sequence as a string. >>>> >>>> Cheers. >>>> Roy. >>>> >>>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>>> >>>>> Hello, >>>>> >>>>> I am curious as to how I am supposed to use SeqIO::fastq to read >>>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>>> seen a method within that module that returns the nucleotide sequence. >>>>> Please, let me know if you have any suggestions! >>>>> >>>>> Thank you very much!! >>>>> >>>> >>>> >>> >>> >>> >> >> > > > From cjfields at illinois.edu Tue Jul 27 11:57:43 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 10:57:43 -0500 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <41845A39-5F63-434A-92E6-86C4CA44C89B@illinois.edu> On Jul 27, 2010, at 10:34 AM, Peter wrote: > On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: >> I'm not certain that I'm using the latest BioPerl, but I can check. In >> the mean time, I'll send you the example data! >> >> @FQ4HLCS02EO12Q region=2 tag=H >> +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC >> +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII >> @FQ4HLCS02EO12T region=2 tag=B >> +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC >> +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 >> > > Hopefully this is just an email problem, but that doesn't look like a > well formatted > FASTQ record to me. Where is the "+" line separating the sequence and qualities? > > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). > > Peter As long as the attachment isn't many MB in size, I don't have a problem. Might get delayed by any spam filters though. chris From David.Messina at sbc.su.se Tue Jul 27 12:18:17 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 27 Jul 2010 10:18:17 -0600 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). Absolutely, please try resending as an attachment, Alan. Dave From david.breimann at gmail.com Sat Jul 24 02:47:43 2010 From: david.breimann at gmail.com (David B) Date: Fri, 23 Jul 2010 23:47:43 -0700 (PDT) Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date Message-ID: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Hi, I'm a bit confused about what is the best way to install and maintain the latest updates for bio perl (I'm working on linux). "Installing Bioperl for Unix" (http://www.bioperl.org/wiki/ Installing_Bioperl_for_Unix) suggests using Build.PL or CPAN, but then again I also know that bioperl is currently developed using github (although I know very little about github). 1. Is installing from github an alternative to Build.pL/CPAN options? 2. Does installing from github simply mean cloning than adding the path to PERL5LIB? That's it? 3. I want to use bp_genbank2gff3.pl for circular genomes and I was told I'd better use the developers release of bioperl because only it handles circular genomes correctly. Does it mean I need to clone ...- dev instead of -live and replace the path accordingly? Thanks, David From david.breimann at gmail.com Sat Jul 24 04:06:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sat, 24 Jul 2010 11:06:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl Message-ID: Hello, I'm trying to convert some genbank files downloaded from NCBI to GFF3 format but I keep getting error messages. My bioperl version (according to perl -MBio::Perl -le 'print Bio::Perl->VERSION;') is 1.0069 (I use github live branch). For example, I am trying to convert CP000249.gbk (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk): $ bp_genbank2gff3.pl CP000249.gbk # Input: CP000249.gbk # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia sp. CcI3, complete genome. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: must be scalar or CODE ref STACK: Error::throw STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/Root.pm:473 STACK: Bio::SeqFeature::Tools::TypeMapper::map_types /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 STACK: /usr/local/bin/bp_genbank2gff3.pl:411 ----------------------------------------------------------- Thanks, David From sc.ncrna at gmail.com Sun Jul 25 09:56:02 2010 From: sc.ncrna at gmail.com (ncRNA) Date: Sun, 25 Jul 2010 06:56:02 -0700 (PDT) Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination Message-ID: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Hi all, I am new to this forum and bioperl. I have a list of mouse genomic regions and would like to get the "corresponding" human genomic sequences, which can be seen from the comparative genomics tracks in the UCSC genome browser. Does anyone have any clue on how to realize this? Thanks in advance, ncRNA From twaddlac at gmail.com Tue Jul 27 12:36:43 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 12:36:43 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: Here's some of the data I would like to parse; the entire file was too big to send via email. Also, if there is some problem with the data, I would appreciate any scripting advice since I am unfortunately a noob :-/ Let me know what you think! Thank you all very much! On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >> Maybe sending this single record as an attachment would work better (is that >> encouraged on this mailing list?). > > Absolutely, please try resending as an attachment, Alan. > > > Dave > > -- Alan Twaddle, B.S. MUC class of 2010 -------------- next part -------------- A non-text attachment was scrubbed... Name: exampleData.fastq Type: application/octet-stream Size: 5510 bytes Desc: not available URL: From cjfields at illinois.edu Tue Jul 27 12:55:26 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 11:55:26 -0500 Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination In-Reply-To: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> References: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Message-ID: <2F614027-844E-43EA-8C01-D7C5C7EBF5E5@illinois.edu> Look at the ensembl API for this (I think compara in particular). chris On Jul 25, 2010, at 8:56 AM, ncRNA wrote: > Hi all, > > I am new to this forum and bioperl. I have a list of mouse genomic > regions and would like to get the "corresponding" human genomic > sequences, which can be seen from the comparative genomics tracks in > the UCSC genome browser. Does anyone have any clue on how to realize > this? > > Thanks in advance, > ncRNA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Tue Jul 27 13:14:48 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 18:14:48 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: <4C4F1408.3090707@gmail.com> Hi Alan, It looks like there wasn't any problem with the earlier e-mail, and that your file is not Fastq, but rather some unusual Fastq-like format - where did you get the file from? Here's a one-liner to convert your file into standard Fastq: perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < exampleData.fastq > standard.fastq I've assumed that your sequences and qualities are all single-line with a + prefix. Once you have a standard Fastq file you should be able to parse it with BioPerl. Roy. On 27/07/2010 17:36, Alan Twaddle wrote: > Here's some of the data I would like to parse; the entire file was too > big to send via email. Also, if there is some problem with the data, I > would appreciate any scripting advice since I am unfortunately a noob > :-/ > > Let me know what you think! > > Thank you all very much! > > On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >>> Maybe sending this single record as an attachment would work better (is that >>> encouraged on this mailing list?). >> >> Absolutely, please try resending as an attachment, Alan. >> >> >> Dave >> >> > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From twaddlac at gmail.com Tue Jul 27 14:57:16 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 14:57:16 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4F1408.3090707@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> <4C4F1408.3090707@gmail.com> Message-ID: Ahh thank you very much, everyone!!!! The data was from a GS-FLX Titanium sequencer but it was parsed out of a database into the format that was the "incorrect" fastq style. However, the script worked (though I'm not confident I understand what it just did) and I have successfully parsed the data out of it via BioPerl! Thanks again!! On Tue, Jul 27, 2010 at 1:14 PM, Roy Chaudhuri wrote: > Hi Alan, > > It looks like there wasn't any problem with the earlier e-mail, and that > your file is not Fastq, but rather some unusual Fastq-like format - where > did you get the file from? > > Here's a one-liner to convert your file into standard Fastq: > > perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < > exampleData.fastq > standard.fastq > > I've assumed that your sequences and qualities are all single-line with a + > prefix. > > Once you have a standard Fastq file you should be able to parse it with > BioPerl. > > Roy. > > On 27/07/2010 17:36, Alan Twaddle wrote: >> >> Here's some of the data I would like to parse; the entire file was too >> big to send via email. Also, if there is some problem with the data, I >> would appreciate any scripting advice since I am unfortunately a noob >> :-/ >> >> Let me know what you think! >> >> Thank you all very much! >> >> On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina >> ?wrote: >>>> >>>> Maybe sending this single record as an attachment would work better (is >>>> that >>>> encouraged on this mailing list?). >>> >>> Absolutely, please try resending as an attachment, Alan. >>> >>> >>> Dave >>> >>> >> >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Alan Twaddle, B.S. MUC class of 2010 From cjm at berkeleybop.org Tue Jul 27 18:14:00 2010 From: cjm at berkeleybop.org (Chris Mungall) Date: Tue, 27 Jul 2010 15:14:00 -0700 Subject: [Bioperl-l] bp_genbank2gff3.pl In-Reply-To: References: Message-ID: Hi David I can't replicate this, but I just pushed a change that gives more informative error messages on the 'circular' branch (same branch I pushed the unflattener temp fix for circular genomes) On Jul 24, 2010, at 1:06 AM, David Breimann wrote: > Hello, > > I'm trying to convert some genbank files downloaded from NCBI to GFF3 > format but I keep getting error messages. > > My bioperl version (according to perl -MBio::Perl -le 'print > Bio::Perl->VERSION;') is 1.0069 (I use github live branch). > > For example, I am trying to convert CP000249.gbk > (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk > ): > > $ bp_genbank2gff3.pl CP000249.gbk > # Input: CP000249.gbk > # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia > sp. CcI3, complete genome. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: must be scalar or CODE ref > STACK: Error::throw > STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/ > Root.pm:473 > STACK: Bio::SeqFeature::Tools::TypeMapper::map_types > /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 > STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 > STACK: /usr/local/bin/bp_genbank2gff3.pl:411 > ----------------------------------------------------------- > > Thanks, > David > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lairdm at sfu.ca Tue Jul 27 19:55:08 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 16:55:08 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ Message-ID: <4C4F71DC.7090503@sfu.ca> Good day, Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? Unfortunately the + sign in the name makes it a little hard to google. :) Thanks. From cjfields at illinois.edu Tue Jul 27 21:29:52 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 20:29:52 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4F71DC.7090503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> Message-ID: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > Good day, > > Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? > > Unfortunately the + sign in the name makes it a little hard to google. :) > > Thanks. Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: http://www.bioperl.org/wiki/HOWTO:BlastPlus chris From maj at fortinbras.us Wed Jul 28 00:51:03 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 28 Jul 2010 00:51:03 -0400 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <9BBF74930A5B477FACC15A4E72E98679@NewLife> >is not backward compatible with StandAloneBlast code, which is a feature, not a >bug ;> If that's not the nicest thing anyone's ever said.... ----- Original Message ----- From: "Chris Fields" To: "Matthew Laird" Cc: Sent: Tuesday, July 27, 2010 9:29 PM Subject: Re: [Bioperl-l] StandAloneBlast & BLAST+ > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the >> docs, and based on my quick testing the answer appears to be no, but does >> Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ > (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and > am trying to get our cluster switched over to it as well. It is not backward > compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get > the github version for this. There is also a bit of online documentation on > this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From lairdm at sfu.ca Wed Jul 28 01:14:05 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 22:14:05 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <4C4FBC9D.2020503@sfu.ca> Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... Thanks for the work guys, we couldn't do it without Bioperl at the core. On 10-07-27 06:29 PM, Chris Fields wrote: > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris From dan.bolser at gmail.com Wed Jul 28 05:59:39 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 10:59:39 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 27 July 2010 14:45, Scott Cain wrote: > Hi Dan, > > You might find the deobfuscator helpful: > > ?http://bioperl.org/cgi-bin/deob_interface.cgi I've tried to use that, but I don't understand how to get it to list the objects that implement a certain interface. > Scott > > > On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: >> On 26 July 2010 16:35, Scott Cain wrote: >>> Hi Dan, >>> >>> I think there are probably several BioPerl classes that implement >>> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >>> for? >> >> A way to find what implements what... something like javadoc for bp. >> >> Really I'm looking for a nice 'ontology' of SeqFeatures. >> >> I was thinking that Contig.pm should implement Bio::SeqFeatureI. >> >> >>> Scott >>> >>> >>> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>>> Which objects implement SeqFeatureI, and how should I find that info? >>>> >>>> Sorry for the gratuitous noobs. >>>> >>>> Cheers, >>>> Dan. >>>> _______________________________________________ >>>> 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 >>> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net > GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 > Ontario Institute for Cancer Research > From dan.bolser at gmail.com Wed Jul 28 06:07:38 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 11:07:38 +0100 Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date In-Reply-To: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> References: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Message-ID: On 24 July 2010 07:47, David B wrote: > Hi, > 1. Is installing from github an alternative to Build.pL/CPAN options? Yes, see this page: http://www.bioperl.org/wiki/Using_Git > 2. Does installing from github simply mean cloning than adding the > path to PERL5LIB? That's it? You could do that, or you could apply 'the mantra': perl Build.PL ./Build test ./Build install Don't forget to complain about all failed tests to the appropriate maintainers. > 3. I want to use bp_genbank2gff3.pl for circular genomes and I was > told I'd better use the developers release of bioperl because only it > handles circular genomes correctly. Does it mean I need to clone ...- > dev instead of -live and replace the path accordingly? AFAICT, bioperl-live is "the developers release". Just don't install "bioperl-dead" ... that's really, really bad. > Thanks, > David > > _______________________________________________ > 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 Jul 28 08:56:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 07:56:41 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4FBC9D.2020503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> <4C4FBC9D.2020503@sfu.ca> Message-ID: <397C1B19-0924-4836-B56F-026779E50943@illinois.edu> I'll be working on a 1.6.2 release very soon (had a slight delay due to problems with circular seqs). But BioPerl-Run and others will also be released as well. On Jul 28, 2010, at 12:14 AM, Matthew Laird wrote: > Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? > > I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... > > Thanks for the work guys, we couldn't do it without Bioperl at the core. > > On 10-07-27 06:29 PM, Chris Fields wrote: >> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: >> >>> Good day, >>> >>> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >>> >>> Unfortunately the + sign in the name makes it a little hard to google. :) >>> >>> Thanks. >> >> Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> >> >> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: >> >> http://www.bioperl.org/wiki/HOWTO:BlastPlus >> >> chris From cjfields at illinois.edu Wed Jul 28 09:33:33 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 08:33:33 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > On 27 July 2010 14:45, Scott Cain wrote: >> Hi Dan, >> >> You might find the deobfuscator helpful: >> >> http://bioperl.org/cgi-bin/deob_interface.cgi > > I've tried to use that, but I don't understand how to get it to list > the objects that implement a certain interface. The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. chris From pengyu.ut at gmail.com Wed Jul 28 18:14:33 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 17:14:33 -0500 Subject: [Bioperl-l] Download sequence by genomic location Message-ID: I could download a sequence by location at genome browser. http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 I know that there are ways to get the sequence. But I don't see a way to get the sequence by location. Could anybody let me know if there is such a function in bioperl? http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database -- Regards, Peng From cjfields at illinois.edu Wed Jul 28 18:39:07 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:39:07 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Not for UCSC (IIRC they specifically requested that we not set this functionality up in case their servers were hit too often). I think Galaxy does this, though, and of course you have EntrezGene and the Ensembl API as alternatives. Might be worth re-checking with the UCSC folks to see what their take is on this now... chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 18:47:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:47:08 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Forgot completely, but this should be possible via Bio::DAS: http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm I have used it myself via GBrowse. chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 18:54:44 2010 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 28 Jul 2010 18:54:44 -0400 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: On Wed, Jul 28, 2010 at 6:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database Hi, Peng. You could use the DAS API at the UCSC browser: http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=1:1,1000 The DAS spec is here: http://www.biodas.org/documents/spec-1.53.html And the UCSC FAQ entry is here: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 You could also download the chromosome files from UCSC and then use a FASTA indexing module from bioperl to allow quick random access to the files. I know you are also an R user, so you could use the BSgenome package and the appropriate genome to do the same thing. Sean From pengyu.ut at gmail.com Wed Jul 28 23:40:14 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 22:40:14 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: I didn't see a document for Bio::Das in my bioperl, $ perldoc Bio::Das No documentation found for "Bio::Das". $ perldoc Bio::Das::SegmentI $ perldoc Bio::Das::FeatureTypeI I thought that maybe my bioperl installation is corrupted. Then I install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I install it by "cpan -f Bio::Das". I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the example. It seems that the there is still something missing. I guess there must be some problem with my bioperl installation. Shall I reinstall it? Is there an easy fix? $ ./main.pl Using password in unencrypted URI against RFC #2396 recommendation at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm line 331. Must have IO::Socket::SSL installed to use https: urls: Can't locate Net/SSLeay.pm in @INC (@INC contains: /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. BEGIN failed--compilation aborted at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. Compilation failed in require at (eval 41) line 3. at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm line 200 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new(5); # timeout of 5 sec my @response = $das->dsn('http://stein.cshl.org/perl/das', 'http://genome.cse.ucsc.edu/cgi-bin/das', 'http://user:pass at www.wormbase.org/db/das', 'https://euclid.well.ox.ac.uk/cgi-bin/das', ); for my $url (@response) { if ($url->is_success) { my @dsns = $url->results; print "$url:\t\n"; foreach (@dsns) { print "\t",$_->url,"\t",$_->description,"\n"; } } else { print "$url: ",$url->error,"\n"; } } On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: > Forgot completely, but this should be possible via Bio::DAS: > > http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm > > I have used it myself via GBrowse. > > chris > > On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > >> I could download a sequence by location at genome browser. >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >> >> I know that there are ways to get the sequence. But I don't see a way >> to get the sequence by location. Could anybody let me know if there is >> such a function in bioperl? >> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >> >> -- >> Regards, >> Peng >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Regards, Peng From cjfields at illinois.edu Thu Jul 29 00:46:56 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 23:46:56 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: It's not part of BioPerl, but is on CPAN: http://search.cpan.org/dist/Bio-Das/ You don't appear to be following the Bio::Das API. The following worked for me: #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new( -source => 'http://genome.cse.ucsc.edu/cgi-bin/das', -dsn => 'hg18', ); my $segment = $das->segment('1:1,100000'); for my $sf ($segment->features) { printf("%s(%s):%d-%d(%d)\n", $sf->display_name, $sf->primary_tag, $sf->start, $sf->end, $sf->strand); } chris On Jul 28, 2010, at 10:40 PM, Peng Yu wrote: > I didn't see a document for Bio::Das in my bioperl, > > $ perldoc Bio::Das > No documentation found for "Bio::Das". > $ perldoc Bio::Das::SegmentI > $ perldoc Bio::Das::FeatureTypeI > > I thought that maybe my bioperl installation is corrupted. Then I > install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I > install it by "cpan -f Bio::Das". > > I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the > example. It seems that the there is still something missing. I guess > there must be some problem with my bioperl installation. > > Shall I reinstall it? Is there an easy fix? > > $ ./main.pl > Using password in unencrypted URI against RFC #2396 recommendation at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm > line 331. > Must have IO::Socket::SSL installed to use https: urls: Can't locate > Net/SSLeay.pm in @INC (@INC contains: > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > BEGIN failed--compilation aborted at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > Compilation failed in require at (eval 41) line 3. > at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm > line 200 > > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::Das; > > my $das = Bio::Das->new(5); # timeout of 5 sec > my @response = $das->dsn('http://stein.cshl.org/perl/das', > 'http://genome.cse.ucsc.edu/cgi-bin/das', > 'http://user:pass at www.wormbase.org/db/das', > 'https://euclid.well.ox.ac.uk/cgi-bin/das', > ); > > for my $url (@response) { > if ($url->is_success) { > my @dsns = $url->results; > print "$url:\t\n"; > foreach (@dsns) { > print "\t",$_->url,"\t",$_->description,"\n"; > } > } else { > print "$url: ",$url->error,"\n"; > } > } > > > On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: >> Forgot completely, but this should be possible via Bio::DAS: >> >> http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm >> >> I have used it myself via GBrowse. >> >> chris >> >> On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: >> >>> I could download a sequence by location at genome browser. >>> >>> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >>> >>> I know that there are ways to get the sequence. But I don't see a way >>> to get the sequence by location. Could anybody let me know if there is >>> such a function in bioperl? >>> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >>> >>> -- >>> Regards, >>> Peng >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > > -- > Regards, > Peng > _______________________________________________ > 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 Thu Jul 29 04:08:46 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 09:08:46 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 28 July 2010 14:33, Chris Fields wrote: > On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > >> On 27 July 2010 14:45, Scott Cain wrote: >>> Hi Dan, >>> >>> You might find the deobfuscator helpful: >>> >>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >> >> I've tried to use that, but I don't understand how to get it to list >> the objects that implement a certain interface. > > The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. OK, so at least I'm not being totally dumb when I can't find this info easily... I'll see if I can script it and add the results to the wiki. > chris From cjfields at illinois.edu Thu Jul 29 09:15:11 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jul 2010 08:15:11 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > On 28 July 2010 14:33, Chris Fields wrote: >> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >> >>> On 27 July 2010 14:45, Scott Cain wrote: >>>> Hi Dan, >>>> >>>> You might find the deobfuscator helpful: >>>> >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> I've tried to use that, but I don't understand how to get it to list >>> the objects that implement a certain interface. >> >> The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. > > OK, so at least I'm not being totally dumb when I can't find this info > easily... I'll see if I can script it and add the results to the wiki. > > >> chris Or, better yet, add it to the /scripts or /examples directory for bioperl-live. Code on the wiki can tend to get lost unless it's in a very accessible place. chris From james-platt at hotmail.co.uk Thu Jul 29 10:18:13 2010 From: james-platt at hotmail.co.uk (James) Date: Thu, 29 Jul 2010 07:18:13 -0700 (PDT) Subject: [Bioperl-l] Newbie question installing on MacOSX Message-ID: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Sorry for the newbie question. I am having trouble installing Bioperl. I'm on MacOSX 10.5.8. I downloaded and installed fink: $ fink --version Package manager version: 0.27.13 Distribution version: 0.9.0 i386 I then downloaded Bioperl-1.6.1, I'm trying to install it from source, as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have Xcode installed etc. '# fink install bioperl-pmXXX' I try this: BioPerl-1.6.1 James$ fink install BioPerl-pm Information about 2521 packages read in 1 seconds. Failed: no package found for specification 'BioPerl-pm'! The version of perl I'm running is 5.8.8, I have tried 'fink install BioPerl588' but this doesn't work either. Thanks very much, James From awitney at sgul.ac.uk Thu Jul 29 11:06:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Thu, 29 Jul 2010 16:06:01 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <08188444-D800-43FD-B1BB-4E1B4332BB46@sgul.ac.uk> Hi James, You are mixing up your installation methods. Either install with fink, or download the source and install from there, not both. I would personally recommend installing it from source or better still install from cpan. Take a look here: http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_Build.PL http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN If you really want to use fink then take a look here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink It looks like the command for this is: fink install bioperl-pm588 but I don't use fink any more so I am not certain of how that works. adam On 29 Jul 2010, at 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 11:23:06 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:23:06 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <4C519CDA.8010008@gmail.com> Hi James, I don't know anything about Macs, but looking here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink shouldn't the command be "fink install bioperl-pm588"? Roy. On 29/07/2010 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 11:36:11 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:36:11 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> Message-ID: <4C519FEB.8050702@gmail.com> Please copy replies to the mailing list, that way others can respond. Try the command: perl -MBio::Seq -e '' If Bioperl is not installed you will get an error message starting "Can't locate Bio/Seq in @INC". If the command just exits silently then BioPerl is installed correctly. Roy. On 29/07/2010 16:29, James Platt wrote: > Hi, > > I tried that, sorry I wasn't clear in the first post. > > James$ fink install bioperl-pm588 > Information about 2521 packages read in 0 seconds. > Failed: no package found for specification 'bioperl-pm588'! > > I think I may have installed it through fink commander. how do i check > in unix that it is in fact installed? > > Thanks, > > James > > On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: > >> Hi James, >> >> I don't know anything about Macs, but looking here: >> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >> >> shouldn't the command be "fink install bioperl-pm588"? >> >> Roy. >> >> On 29/07/2010 15:18, James wrote: >>> Sorry for the newbie question. >>> >>> I am having trouble installing Bioperl. >>> >>> I'm on MacOSX 10.5.8. >>> >>> I downloaded and installed fink: >>> >>> $ fink --version >>> Package manager version: 0.27.13 >>> Distribution version: 0.9.0 i386 >>> >>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>> source, >>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>> Xcode installed etc. >>> >>> '# fink install bioperl-pmXXX' >>> >>> I try this: >>> >>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>> >>> Information about 2521 packages read in 1 seconds. >>> Failed: no package found for specification 'BioPerl-pm'! >>> >>> >>> The version of perl I'm running is 5.8.8, I have tried 'fink install >>> BioPerl588' but this doesn't work either. >>> >>> Thanks very much, >>> >>> James >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From james-platt at hotmail.co.uk Thu Jul 29 12:11:48 2010 From: james-platt at hotmail.co.uk (James Platt) Date: Thu, 29 Jul 2010 17:11:48 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <4C519FEB.8050702@gmail.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> <4C519FEB.8050702@gmail.com> Message-ID: when I'm in the directory it exits silently. When I'm not... James$ perl -MBio::Seq -e '' Can't locate Bio/Seq.pm in @INC (@INC contains: /sw/lib/perl5/darwin- thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/ Updates/5.8.8 /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 .). BEGIN failed--compilation aborted. I guess I need to try install it again. J On 29 Jul 2010, at 16:36, Roy Chaudhuri wrote: > Please copy replies to the mailing list, that way others can respond. > > Try the command: > perl -MBio::Seq -e '' > > If Bioperl is not installed you will get an error message starting > "Can't locate Bio/Seq in @INC". If the command just exits silently > then BioPerl is installed correctly. > > Roy. > > On 29/07/2010 16:29, James Platt wrote: >> Hi, >> >> I tried that, sorry I wasn't clear in the first post. >> >> James$ fink install bioperl-pm588 >> Information about 2521 packages read in 0 seconds. >> Failed: no package found for specification 'bioperl-pm588'! >> >> I think I may have installed it through fink commander. how do i >> check >> in unix that it is in fact installed? >> >> Thanks, >> >> James >> >> On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: >> >>> Hi James, >>> >>> I don't know anything about Macs, but looking here: >>> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >>> >>> shouldn't the command be "fink install bioperl-pm588"? >>> >>> Roy. >>> >>> On 29/07/2010 15:18, James wrote: >>>> Sorry for the newbie question. >>>> >>>> I am having trouble installing Bioperl. >>>> >>>> I'm on MacOSX 10.5.8. >>>> >>>> I downloaded and installed fink: >>>> >>>> $ fink --version >>>> Package manager version: 0.27.13 >>>> Distribution version: 0.9.0 i386 >>>> >>>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>>> source, >>>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>>> Xcode installed etc. >>>> >>>> '# fink install bioperl-pmXXX' >>>> >>>> I try this: >>>> >>>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>>> >>>> Information about 2521 packages read in 1 seconds. >>>> Failed: no package found for specification 'BioPerl-pm'! >>>> >>>> >>>> The version of perl I'm running is 5.8.8, I have tried 'fink >>>> install >>>> BioPerl588' but this doesn't work either. >>>> >>>> Thanks very much, >>>> >>>> James >>>> >>>> _______________________________________________ >>>> 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 Thu Jul 29 14:17:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 19:17:42 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 29 July 2010 14:15, Chris Fields wrote: > On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > >> On 28 July 2010 14:33, Chris Fields wrote: >>> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >>> >>>> On 27 July 2010 14:45, Scott Cain wrote: >>>>> Hi Dan, >>>>> >>>>> You might find the deobfuscator helpful: >>>>> >>>>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> I've tried to use that, but I don't understand how to get it to list >>>> the objects that implement a certain interface. >>> >>> The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. >> >> OK, so at least I'm not being totally dumb when I can't find this info >> easily... I'll see if I can script it and add the results to the wiki. >> >> >>> chris > > Or, better yet, add it to the /scripts or /examples directory for bioperl-live. ?Code on the wiki can tend to get lost unless it's in a very accessible place. I meant I'd add the results to the wiki. Nice idea to add the code to the distro. > chris From frederic.romagne at gmail.com Fri Jul 30 00:59:35 2010 From: frederic.romagne at gmail.com (=?ISO-8859-1?Q?Fr=E9d=E9ric_Romagn=E9?=) Date: Fri, 30 Jul 2010 14:59:35 +1000 Subject: [Bioperl-l] phyloxml and element order Message-ID: Hi, I'm using bioperl to create phyloxml trees, after few tentatives, i got my tree with all the element/attributes i want but when I write the tree, element are not written following the order specified in the XSD Schema. For example, i got : Loxosceles intermedia Araneomorphae Sicariidae 969 HAAERADSRKPIWDIAHMVNDLELVD Araneomorphae Sicariidae The program forester complains that should be written before the element. According to http://phyloxml.wordpress.com/2009/11/25/order-of-elements-in-phyloxml this is what bioperl is supposed to do. All my element/attributes are set before writing the tree using 'add_Annotation', 'add_tag_value' and 'sequence' methods from a Bio::Tree::AnnotatableNode object, so i think the error comes from the write_tree method. Any help would be appreciated. Thank you, Fred From com505 at york.ac.uk Fri Jul 30 05:37:11 2010 From: com505 at york.ac.uk (Carrie O'Malley) Date: Fri, 30 Jul 2010 10:37:11 +0100 Subject: [Bioperl-l] installing bioperl Message-ID: Hi there I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. I am not able to complete the installation as every time I get: Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have tried using both methods to install into a local folder and get the same thing !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/home/users/carrieomalley/bin' mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( Many thanks in advance Carrie Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: Data::Stag is not installed (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) CPAN: Storable loaded ok (v2.18) Going to read /Users/carrieomalley/.cpan/Metadata Database was generated on Sat, 10 Jul 2010 11:27:04 GMT Running install for module 'Data::Stag' 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok x Data-Stag-0.11/ x Data-Stag-0.11/c-ext/ x Data-Stag-0.11/c-ext/README.c-ext x Data-Stag-0.11/c-ext/staglib.c x Data-Stag-0.11/c-ext/staglib.h x Data-Stag-0.11/Changes x Data-Stag-0.11/Data/ x Data-Stag-0.11/Data/Stag/ x Data-Stag-0.11/Data/Stag/Arr2HTML.pm x Data-Stag-0.11/Data/Stag/Base.pm x Data-Stag-0.11/Data/Stag/BaseGenerator.pm x Data-Stag-0.11/Data/Stag/BaseHandler.pm x Data-Stag-0.11/Data/Stag/ChainHandler.pm x Data-Stag-0.11/Data/Stag/DTDWriter.pm x Data-Stag-0.11/Data/Stag/GraphHandler.pm x Data-Stag-0.11/Data/Stag/HashDB.pm x Data-Stag-0.11/Data/Stag/IndentParser.pm x Data-Stag-0.11/Data/Stag/IndentWriter.pm x Data-Stag-0.11/Data/Stag/ITextParser.pm x Data-Stag-0.11/Data/Stag/ITextWriter.pm x Data-Stag-0.11/Data/Stag/null.pm x Data-Stag-0.11/Data/Stag/PerlWriter.pm x Data-Stag-0.11/Data/Stag/PodParser.pm x Data-Stag-0.11/Data/Stag/SAX2Stag.pm x Data-Stag-0.11/Data/Stag/Simple.pm x Data-Stag-0.11/Data/Stag/StagDB.pm x Data-Stag-0.11/Data/Stag/StagI.pm x Data-Stag-0.11/Data/Stag/StagImpl.pm x Data-Stag-0.11/Data/Stag/SxprParser.pm x Data-Stag-0.11/Data/Stag/SxprWriter.pm x Data-Stag-0.11/Data/Stag/Util.pm x Data-Stag-0.11/Data/Stag/Writer.pm x Data-Stag-0.11/Data/Stag/XMLParser.pm x Data-Stag-0.11/Data/Stag/XMLWriter.pm x Data-Stag-0.11/Data/Stag/XSLHandler.pm x Data-Stag-0.11/Data/Stag/XSLTHandler.pm x Data-Stag-0.11/Data/Stag.pm x Data-Stag-0.11/dev/ x Data-Stag-0.11/dev/create-manifest.sh x Data-Stag-0.11/dev/data-stag.spec x Data-Stag-0.11/dev/mkspec.pl x Data-Stag-0.11/elisp/ x Data-Stag-0.11/elisp/itext-mode.el x Data-Stag-0.11/homepage/ x Data-Stag-0.11/homepage/archBIG.png x Data-Stag-0.11/homepage/dbstag-tutorial.sgml x Data-Stag-0.11/homepage/images/ x Data-Stag-0.11/homepage/images/k-schema-diagram.png x Data-Stag-0.11/homepage/images/rr-schema-diagram.png x Data-Stag-0.11/homepage/index.html x Data-Stag-0.11/homepage/makefile x Data-Stag-0.11/homepage/mk.sh x Data-Stag-0.11/homepage/mkpodhtml.pl x Data-Stag-0.11/homepage/mkscriptdoc.pl x Data-Stag-0.11/homepage/script-docs/ x Data-Stag-0.11/homepage/script-docs/selectall_html.html x Data-Stag-0.11/homepage/script-docs/selectall_xml.html x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html x Data-Stag-0.11/homepage/script-docs/stag-db.html x Data-Stag-0.11/homepage/script-docs/stag-diff.html x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html x Data-Stag-0.11/homepage/script-docs/stag-elcount.html x Data-Stag-0.11/homepage/script-docs/stag-eval.html x Data-Stag-0.11/homepage/script-docs/stag-filter.html x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html x Data-Stag-0.11/homepage/script-docs/stag-flatten.html x Data-Stag-0.11/homepage/script-docs/stag-grep.html x Data-Stag-0.11/homepage/script-docs/stag-handle.html x Data-Stag-0.11/homepage/script-docs/stag-ir.html x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html x Data-Stag-0.11/homepage/script-docs/stag-join.html x Data-Stag-0.11/homepage/script-docs/stag-merge.html x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html x Data-Stag-0.11/homepage/script-docs/stag-parse.html x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html x Data-Stag-0.11/homepage/script-docs/stag-query.html x Data-Stag-0.11/homepage/script-docs/stag-show-template.html x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html x Data-Stag-0.11/homepage/script-docs/stag-splitter.html x Data-Stag-0.11/homepage/script-docs/stag-storenode.html x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html x Data-Stag-0.11/homepage/script-docs/stag-view.html x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html x Data-Stag-0.11/homepage/script-list.html x Data-Stag-0.11/homepage/stag-db-tutorial.html x Data-Stag-0.11/homepage/stag-poster.html x Data-Stag-0.11/INSTALL x Data-Stag-0.11/Makefile.PL x Data-Stag-0.11/MANIFEST x Data-Stag-0.11/META.yml x Data-Stag-0.11/README x Data-Stag-0.11/scripts/ x Data-Stag-0.11/scripts/stag-autoschema.pl x Data-Stag-0.11/scripts/stag-db.pl x Data-Stag-0.11/scripts/stag-diff.pl x Data-Stag-0.11/scripts/stag-drawtree.pl x Data-Stag-0.11/scripts/stag-elcount.pl x Data-Stag-0.11/scripts/stag-eval.pl x Data-Stag-0.11/scripts/stag-filter.pl x Data-Stag-0.11/scripts/stag-findsubtree.pl x Data-Stag-0.11/scripts/stag-flatten.pl x Data-Stag-0.11/scripts/stag-grep.pl x Data-Stag-0.11/scripts/stag-handle.pl x Data-Stag-0.11/scripts/stag-itext2simple.pl x Data-Stag-0.11/scripts/stag-itext2sxpr.pl x Data-Stag-0.11/scripts/stag-itext2xml.pl x Data-Stag-0.11/scripts/stag-join.pl x Data-Stag-0.11/scripts/stag-merge.pl x Data-Stag-0.11/scripts/stag-mogrify.pl x Data-Stag-0.11/scripts/stag-parse.pl x Data-Stag-0.11/scripts/stag-query.pl x Data-Stag-0.11/scripts/stag-splitter.pl x Data-Stag-0.11/scripts/stag-view.pl x Data-Stag-0.11/scripts/stag-xml2itext.pl x Data-Stag-0.11/scripts/stag-xmlsplit.pl x Data-Stag-0.11/t/ x Data-Stag-0.11/t/animal.x x Data-Stag-0.11/t/autoschema.t x Data-Stag-0.11/t/barfly.x x Data-Stag-0.11/t/bio.x x Data-Stag-0.11/t/chainhandler.t x Data-Stag-0.11/t/collapse.x x Data-Stag-0.11/t/data/ x Data-Stag-0.11/t/data/attrs.xml x Data-Stag-0.11/t/data/bf.txt x Data-Stag-0.11/t/data/eco.el x Data-Stag-0.11/t/data/eco.itext x Data-Stag-0.11/t/data/homol.itext x Data-Stag-0.11/t/data/persons.el x Data-Stag-0.11/t/db.t x Data-Stag-0.11/t/emptytag.t x Data-Stag-0.11/t/get.t x Data-Stag-0.11/t/graph.x x Data-Stag-0.11/t/handlers.t x Data-Stag-0.11/t/handlers2.t x Data-Stag-0.11/t/handlers2.x x Data-Stag-0.11/t/hashdb.t x Data-Stag-0.11/t/hashdb.x x Data-Stag-0.11/t/homol.t x Data-Stag-0.11/t/lisp.x x Data-Stag-0.11/t/parsestr.t x Data-Stag-0.11/t/path.x x Data-Stag-0.11/t/path2.x x Data-Stag-0.11/t/qmatch.t x Data-Stag-0.11/t/roundtrip-attrs.t x Data-Stag-0.11/t/set-attrs.t x Data-Stag-0.11/t/set.t x Data-Stag-0.11/t/sxpr.t x Data-Stag-0.11/t/unhash.t x Data-Stag-0.11/t/unset.t x Data-Stag-0.11/t/write.t x Data-Stag-0.11/t/xml1.t x Data-Stag-0.11/t/xml2.t CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz External Module XML::LibXSLT, XSLT, is not installed on this computer. Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations External Module XML::Parser::PerlSAX, SAX Handler, is not installed on this computer. Data::Stag::XMLParser in Data::Stag needs it for parsing XML External Module GD, Graphical Drawing Toolkit, is not installed on this computer. stag-drawtree.pl in Data::Stag needs it for drawing trees External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer. Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs External Module Tk, Tk, is not installed on this computer. stag-view.pl in Data::Stag needs it for tree viewer Information: There are some external packages and perl modules, listed above, which stag uses. This only effects the functionality which is listed above: the rest of stag will work fine, which includes nearly all of the core functionality. Enjoy the rest of stag, which you can use after going 'make install' Checking if your kit is complete... Looks good Writing Makefile for Data Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm cp Data/Stag.pm blib/lib/Data/Stag.pm cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm cp scripts/stag-view.pl blib/script/stag-view.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl cp scripts/stag-grep.pl blib/script/stag-grep.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl cp scripts/stag-merge.pl blib/script/stag-merge.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl cp scripts/stag-parse.pl blib/script/stag-parse.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl cp scripts/stag-join.pl blib/script/stag-join.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl cp scripts/stag-db.pl blib/script/stag-db.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl cp scripts/stag-filter.pl blib/script/stag-filter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl cp scripts/stag-handle.pl blib/script/stag-handle.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl cp scripts/stag-query.pl blib/script/stag-query.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl cp scripts/stag-flatten.pl blib/script/stag-flatten.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl cp scripts/stag-splitter.pl blib/script/stag-splitter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl cp scripts/stag-diff.pl blib/script/stag-diff.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl Manifying blib/man1/stag-view.pl.1 Manifying blib/man1/stag-mogrify.pl.1 Manifying blib/man1/stag-grep.pl.1 Manifying blib/man1/stag-handle.pl.1 Manifying blib/man1/stag-drawtree.pl.1 Manifying blib/man1/stag-query.pl.1 Manifying blib/man1/stag-merge.pl.1 Manifying blib/man1/stag-parse.pl.1 Manifying blib/man1/stag-findsubtree.pl.1 Manifying blib/man1/stag-join.pl.1 Manifying blib/man1/stag-autoschema.pl.1 Manifying blib/man1/stag-db.pl.1 Manifying blib/man1/stag-flatten.pl.1 Manifying blib/man1/stag-splitter.pl.1 Manifying blib/man1/stag-diff.pl.1 Manifying blib/man1/stag-filter.pl.1 Manifying blib/man3/Data::Stag::StagDB.3pm Manifying blib/man3/Data::Stag::SxprWriter.3pm Manifying blib/man3/Data::Stag.3pm Manifying blib/man3/Data::Stag::ChainHandler.3pm Manifying blib/man3/Data::Stag::IndentParser.3pm Manifying blib/man3/Data::Stag::Simple.3pm Manifying blib/man3/Data::Stag::SAX2Stag.3pm Manifying blib/man3/Data::Stag::Arr2HTML.3pm Manifying blib/man3/Data::Stag::XSLHandler.3pm Manifying blib/man3/Data::Stag::PerlWriter.3pm Manifying blib/man3/Data::Stag::XSLTHandler.3pm Manifying blib/man3/Data::Stag::DTDWriter.3pm Manifying blib/man3/Data::Stag::Writer.3pm Manifying blib/man3/Data::Stag::XMLWriter.3pm Manifying blib/man3/Data::Stag::GraphHandler.3pm Manifying blib/man3/Data::Stag::XMLParser.3pm Manifying blib/man3/Data::Stag::StagImpl.3pm Manifying blib/man3/Data::Stag::PodParser.3pm Manifying blib/man3/Data::Stag::BaseGenerator.3pm Manifying blib/man3/Data::Stag::IndentWriter.3pm Manifying blib/man3/Data::Stag::HashDB.3pm Manifying blib/man3/Data::Stag::null.3pm Manifying blib/man3/Data::Stag::ITextParser.3pm Manifying blib/man3/Data::Stag::BaseHandler.3pm Manifying blib/man3/Data::Stag::ITextWriter.3pm Manifying blib/man3/Data::Stag::SxprParser.3pm CMUNGALL/Data-Stag-0.11.tar.gz make -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/autoschema.........ok t/chainhandler.......ok t/db.................ok t/emptytag...........ok 3/3 skipped: various reasons t/get................ok t/handlers...........ok t/handlers2..........ok 1/9 skipped: various reasons t/hashdb.............ok t/homol..............ok t/parsestr...........ok 6/6 skipped: various reasons t/qmatch.............ok t/roundtrip-attrs....ok 5/5 skipped: various reasons t/set-attrs..........ok 3/3 skipped: various reasons t/set................ok t/sxpr...............ok t/unhash.............ok t/unset..............ok t/write..............ok t/xml1...............ok 7/7 skipped: various reasons t/xml2...............ok 4/4 skipped: various reasons All tests successful, 29 subtests skipped. Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) CMUNGALL/Data-Stag-0.11.tar.gz make test -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make install Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1 make: *** [pure_site_install] Error 13 CMUNGALL/Data-Stag-0.11.tar.gz make install -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state *** (back in Bioperl Build.PL) *** Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n - ERROR: You chose to install Data::Stag but it failed to install * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Spreadsheet::ParseExcel is not installed (wanted for parsing Excel files, used by Bio::SeqIO::excel) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite Graph is not installed (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) * Optional prerequisite SVG::Graph is not installed (wanted for creating SVG images, used by Bio::TreeIO::svggraph) * Optional prerequisite SOAP::Lite is not installed (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Convert::Binary::C is not installed (wanted for strider functionality, used by Bio::SeqIO::strider) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite XML::Twig is not installed (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) * Optional prerequisite Set::Scalar is not installed (wanted for proper operation, used by Bio::Tree::Compatible) * Optional prerequisite XML::Parser::PerlSAX is not installed (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite Clone is not installed (wanted for cloning objects, used by Bio::Tools::Primer3) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: BioDBGFF.................disabled * MySQL, Pg nor Oracle DBI drivers are installed BioDBSeqFeature_mysql....disabled - DBD::mysql is not installed Network..................enabled BioDBSeqFeature_BDB......enabled Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] n - will not run internet-requiring tests Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'BioPerl' version '1.006000' Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok 1/28 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- # Looks like you planned 28 tests but only ran 7. # Looks like your test died just after 7. t/AlignIO/AlignIO............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 8-28 Failed 21/28 tests, 25.00% okay t/AlignIO/arp................................ok 1/48 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- # Looks like you planned 48 tests but only ran 2. # Looks like your test died just after 2. t/AlignIO/arp................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-48 Failed 46/48 tests, 4.17% okay 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......................ok 1/159 # Failed test 'use Bio::Annotation::TagTree;' # at t/Annotation/Annotation.t line 20. # Tried to use 'Bio::Annotation::TagTree'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. # Compilation failed in require at (eval 37) line 2. # BEGIN failed--compilation aborted at (eval 37) line 2. t/Annotation/Annotation......................NOK 9/159 # Failed test 'default itext' # at t/Annotation/Annotation.t line 307. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' # Failed test 'itext' # at t/Annotation/Annotation.t line 315. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. # Looks like you planned 159 tests but only ran 119. # Looks like you failed 3 tests of 119 run. # Looks like your test died just after 119. t/Annotation/Annotation......................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 9, 117, 119-159 Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................ok 1/51 # Failed (TODO) test at t/Assembly/Assembly.t line 35. t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok 1/24 skipped: various reasons t/Biblio/References..........................ok t/Biblio/biofetch............................skipped all skipped: Network tests have not been requested t/Biblio/eutils..............................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/ClusterIO/ClusterIO........................ok 8/12 skipped: various reasons t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/ClusterIO/SequenceFamily.t:16 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. # Looks like you planned 19 tests but only ran 2. # Looks like your test died just after 2. t/ClusterIO/SequenceFamily...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-19 Failed 17/19 tests, 10.53% okay 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 11/279 skipped: various reasons t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 STACK: t/LocalDB/Flat.t:89 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. # Looks like you planned 24 tests but only ran 14. # Looks like your test died just after 14. t/LocalDB/Flat...............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-24 Failed 10/24 tests, 58.33% okay t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 STACK: t/LocalDB/Index.t:91 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. # Looks like you planned 64 tests but only ran 31. # Looks like your test died just after 31. t/LocalDB/Index..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 32-64 Failed 33/64 tests, 48.44% okay t/LocalDB/Registry...........................ok 9/14 skipped: various reasons t/LocalDB/SeqFeature.........................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok 19/267 skipped: various reasons 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 10/14 skipped: various reasons t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok 10/29 skipped: various reasons 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..................................ok t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok 4/46 skipped: various reasons t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................skipped all skipped: Network tests have not been requested t/RemoteDB/CUTG..............................ok 14/37 skipped: various reasons t/RemoteDB/DB................................skipped all skipped: Network tests have not been requested t/RemoteDB/EMBL..............................skipped all skipped: Network tests have not been requested t/RemoteDB/EUtilities........................skipped all skipped: Network tests have not been requested t/RemoteDB/HIV/HIV...........................ok 13/30 skipped: various reasons t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok 10/41 skipped: various reasons t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok 10/16 skipped: various reasons t/RemoteDB/SeqHound..........................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqRead_fail......................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqVersion........................ok 8/10 skipped: various reasons t/RemoteDB/Taxonomy..........................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................ok 1/18 # Failed (TODO) test at t/Restriction/IO.t line 31. t/Restriction/IO.............................ok 3/18 skipped: various reasons t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................ok 2/31 skipped: various reasons t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped all 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.............................ok 1/1093 # Failed (TODO) test at t/SearchIO/blast.t line 527. # '0.852' # > # '0.9' # Failed (TODO) test at t/SearchIO/blast.t line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................ok 1/289 # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................ok 1/298 # Failed (TODO) test at t/SearchIO/blastxml.t line 258. # got: undef # expected: '31984247' # Failed (TODO) test at t/SearchIO/blastxml.t line 259. # got: undef # expected: '88780' # Failed (TODO) test at t/SearchIO/blastxml.t line 260. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok 4/45 skipped: various reasons 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...........................ok 1/116 # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. # got: 'Bio::Location::Simple=HASH(0x100838ce8)' # expected: undef # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test at t/Seq/LocatableSeq.t 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 all 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 all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok 7/214 skipped: various reasons t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqIO/Handler.t:20 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. # Looks like you planned 550 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/Handler..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-550 Failed 549/550 tests, 0.18% okay t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped all 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..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped all skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ # Failed test 'use Bio::SeqIO::chaos;' # at t/SeqIO/chaos.t line 15. # Tried to use 'Bio::SeqIO::chaos'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. # Looks like you failed 1 test of 8. t/SeqIO/chaos................................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/8 tests, 87.50% okay t/SeqIO/chaosxml.............................skipped all skipped: The optional module Data::Stag (or dependencies thereof) was not installed t/SeqIO/ctf..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped all 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 all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................ok 1/17 # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 54. # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped all 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 all 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 all 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..................................ok 1/59 # Failed (TODO) test 'accuracies' # at t/SeqIO/scf.t line 78. # got: 'ARRAY(0x100ac5648)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ # Failed test 'use Bio::SeqIO::swiss;' # at t/SeqIO/swiss.t line 12. # Tried to use 'Bio::SeqIO::swiss'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. # Looks like you planned 240 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqIO/swiss................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-240 Failed 240/240 tests, 0.00% okay t/SeqIO/tab..................................ok t/SeqIO/table................................ok 112/450 skipped: various reasons t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped all 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 1/49Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqTools/GuessSeqFormat.t:62 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time t/SeqTools/GuessSeqFormat....................NOK 25/49 # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. # ' # at t/SeqTools/GuessSeqFormat.t line 71. # got: '0' # expected: '1' # Looks like you planned 49 tests but ran 1 extra. # Looks like you failed 1 test of 50 run. t/SeqTools/GuessSeqFormat....................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED tests 25, 50 Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok 5/21 skipped: various reasons t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped all 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 all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut..............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos.............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/Tools/Analysis/Protein/Scansite.t:23 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. # Looks like you planned 14 tests but only ran 4. # Looks like your test died just after 4. t/Tools/Analysis/Protein/Scansite............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-14 Failed 10/14 tests, 28.57% okay t/Tools/Analysis/Protein/Sopma...............ok 12/16 skipped: various reasons 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 all 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......................skipped all skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast..................ok 12/45 skipped: various reasons 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 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 all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok 2/74 skipped: various reasons t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................ok t/Tree/TreeIO/svggraph.......................ok 3/4 skipped: various reasons 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 15/26 skipped: various reasons Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/AlignIO/AlignIO.t 255 65280 28 42 8-28 t/AlignIO/arp.t 255 65280 48 92 3-48 t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 t/LocalDB/Flat.t 255 65280 24 20 15-24 t/LocalDB/Index.t 255 65280 64 66 32-64 t/SeqIO/Handler.t 255 65280 550 1098 2-550 t/SeqIO/chaos.t 1 256 8 1 1 t/SeqIO/swiss.t 255 65280 240 479 1-240 t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 57 tests and 313 subtests skipped. Failed 11/318 test scripts. 970/17228 subtests failed. Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) Failed 11/318 test programs. 970/17228 subtests failed. Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 From robfsouza at gmail.com Fri Jul 30 09:54:08 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 30 Jul 2010 09:54:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Did you try, as root, ./Build.pl --install_base /opt/local ? Also, check the INSTALL file at the root of the bioperl distribution. Robson On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > ?I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > ?- ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > ?is not installed on this computer. > ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > ?is not installed on this computer. > ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > ?is not installed on this computer. > ?stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > ?is not installed on this computer. > ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > ?is not installed on this computer. > ?stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > ? There are some external packages and perl modules, listed above, which > ? stag uses. This only effects the functionality which is listed above: > ? the rest of stag will work fine, which includes nearly all of the > ? core functionality. > > ? Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > ? ? ? ?3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > ? ? ? ?1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > ? ? ? ?6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > ? ? ? ?5/5 skipped: various reasons > t/set-attrs..........ok > ? ? ? ?3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > ? ? ? ?7/7 skipped: various reasons > t/xml2...............ok > ? ? ? ?4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at -e line 1 > make: *** [pure_site_install] Error 13 > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make install ?-- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > ?- ERROR: You chose to install Data::Stag but it failed to install > ?* Optional prerequisite Ace is not installed > ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > ?* Optional prerequisite Spreadsheet::ParseExcel is not installed > ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) > ?* Optional prerequisite Math::Random is not installed > ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > ?* Optional prerequisite Graph is not installed > ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > ?* Optional prerequisite SVG::Graph is not installed > ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > ?* Optional prerequisite SOAP::Lite is not installed > ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed > ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > ?* Optional prerequisite GraphViz is not installed > ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > ?* Optional prerequisite Array::Compare is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite Convert::Binary::C is not installed > ? (wanted for strider functionality, used by Bio::SeqIO::strider) > ?* Optional prerequisite Algorithm::Munkres is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite XML::Twig is not installed > ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > ?* Optional prerequisite Set::Scalar is not installed > ? (wanted for proper operation, used by Bio::Tree::Compatible) > ?* Optional prerequisite XML::Parser::PerlSAX is not installed > ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > ?* Optional prerequisite XML::SAX::Writer is not installed > ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) > ?* Optional prerequisite Clone is not installed > ? (wanted for cloning objects, used by Bio::Tools::Primer3) > ?* Optional prerequisite XML::DOM::XPath is not installed > ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > ?* Optional prerequisite PostScript::TextBlock is not installed > ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > ?BioDBGFF.................disabled > ? ?* MySQL, Pg nor Oracle DBI drivers are installed > ?BioDBSeqFeature_mysql....disabled > ? ?- DBD::mysql is not installed > ?Network..................enabled > ?BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > ?- will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > ?- will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > ? ? ? ?Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > ? ? ? ?Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # ? Failed test 'use Bio::Annotation::TagTree;' > # ? at t/Annotation/Annotation.t line 20. > # ? ? Tried to use 'Bio::Annotation::TagTree'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # ? Failed test 'default itext' > # ? at t/Annotation/Annotation.t line 307. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > > # ? Failed test 'itext' > # ? at t/Annotation/Annotation.t line 315. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > ? ? ? ?1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > ? ? ? ?8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > ? ? ? ?Failed 17/19 tests, 10.53% okay > 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 > ? ? ? ?11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > ? ? ? ?Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > ? ? ? ?Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > ? ? ? ?9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > ? ? ? ?19/267 skipped: various reasons > 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 > ? ? ? ?10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > ? ? ? ?10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > ? ? ? ?4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > ? ? ? ?14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > ? ? ? ?13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > ? ? ? ?10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > ? ? ? ?10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > ? ? ? ?8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # ? Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > ? ? ? ?3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > ? ? ? ?2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > ? ? ? ?all 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.............................ok 1/1093 > # ? Failed (TODO) test at t/SearchIO/blast.t line 527. > # ? ? '0.852' > # ? ? ? ? > > # ? ? '0.9' > > # ? Failed (TODO) test at t/SearchIO/blast.t line 528. > # ? ? '1.599' > # ? ? ? ? <= > # ? ? '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # ? ? ? ? ?got: '0.946' > # ? ? expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # ? ? ? ? ?got: undef > # ? ? expected: '31984247' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # ? ? ? ? ?got: undef > # ? ? expected: '88780' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # ? ? ? ? ?got: undef > # ? ? expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > ? ? ? ?4/45 skipped: various reasons > 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...........................ok 1/116 > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # ? ? expected: undef > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # ? ? ? ? ?got: '\-\.=~' > # ? ? expected: '-\?' > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > ? ? ? ?7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > ? ? ? ?Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > ? ? ? ?all 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..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # ? Failed test 'use Bio::SeqIO::chaos;' > # ? at t/SeqIO/chaos.t line 15. > # ? ? Tried to use 'Bio::SeqIO::chaos'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > ? ? ? ?Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # ? Failed (TODO) test 'primary_id' > # ? at t/SeqIO/gcg.t line 54. > # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # ? ? expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > ? ? ? ?all 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 > ? ? ? ?all 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 > ? ? ? ?all 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..................................ok 1/59 > # ? Failed (TODO) test 'accuracies' > # ? at t/SeqIO/scf.t line 78. > # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' > # ? ? expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # ? Failed test 'use Bio::SeqIO::swiss;' > # ? at t/SeqIO/swiss.t line 12. > # ? ? Tried to use 'Bio::SeqIO::swiss'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > ? ? ? ?Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > ? ? ? ?112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # ? at t/SeqTools/GuessSeqFormat.t line 71. > # ? ? ? ? ?got: '0' > # ? ? expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > ? ? ? ?5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > ? ? ? ?Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > ? ? ? ?12/16 skipped: various reasons > 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 > ? ? ? ?all 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......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > ? ? ? ?12/45 skipped: various reasons > 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 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 > ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > ? ? ? ?2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > ? ? ? ?3/4 skipped: various reasons > 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 > ? ? ? ?15/26 skipped: various reasons > Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 > t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 > t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 > t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 > t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 > t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 > t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 > t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 > t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 > t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 > t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > 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 Fri Jul 30 11:26:12 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Fri, 30 Jul 2010 16:26:12 +0100 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: <70A35EB0-D004-4B7A-A239-D9EA7F9EA206@sgul.ac.uk> It looks like it is trying to install and failing because of lack of permissions. I would recommend you try the cpan route like this: perl -MCPAN -e shell then from the cpan prompt, set a few things up (only need to do this once): cpan> o conf make_install_make_command 'sudo make' cpan> o conf mbuild_install_build_command 'sudo ./Build' cpan> o conf commit cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz .... and keep an eye on it... it will ask for a password early on to allow it to install into the right directories. Or you if you want to retry your current method you could do this sudo perl ./Build.pl HTH adam On 30 Jul 2010, at 10:37, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > - ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > is not installed on this computer. > Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > is not installed on this computer. > Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > is not installed on this computer. > stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > is not installed on this computer. > Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > is not installed on this computer. > stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > There are some external packages and perl modules, listed above, which > stag uses. This only effects the functionality which is listed above: > the rest of stag will work fine, which includes nearly all of the > core functionality. > > Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > CMUNGALL/Data-Stag-0.11.tar.gz > make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > 3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > 1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > 6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > 5/5 skipped: various reasons > t/set-attrs..........ok > 3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > 7/7 skipped: various reasons > t/xml2...............ok > 4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) > CMUNGALL/Data-Stag-0.11.tar.gz > make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at -e line 1 > make: *** [pure_site_install] Error 13 > CMUNGALL/Data-Stag-0.11.tar.gz > make install -- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > - ERROR: You chose to install Data::Stag but it failed to install > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > * Optional prerequisite Spreadsheet::ParseExcel is not installed > (wanted for parsing Excel files, used by Bio::SeqIO::excel) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite Graph is not installed > (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > * Optional prerequisite SVG::Graph is not installed > (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > * Optional prerequisite SOAP::Lite is not installed > (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > * Optional prerequisite Bio::ASN1::EntrezGene is not installed > (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Convert::Binary::C is not installed > (wanted for strider functionality, used by Bio::SeqIO::strider) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite XML::Twig is not installed > (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > * Optional prerequisite Set::Scalar is not installed > (wanted for proper operation, used by Bio::Tree::Compatible) > * Optional prerequisite XML::Parser::PerlSAX is not installed > (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > * Optional prerequisite XML::SAX::Writer is not installed > (wanted for writing xml, used by Bio::SeqIO::tigrxml) > * Optional prerequisite Clone is not installed > (wanted for cloning objects, used by Bio::Tools::Primer3) > * Optional prerequisite XML::DOM::XPath is not installed > (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > * Optional prerequisite PostScript::TextBlock is not installed > (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > BioDBGFF.................disabled > * MySQL, Pg nor Oracle DBI drivers are installed > BioDBSeqFeature_mysql....disabled > - DBD::mysql is not installed > Network..................enabled > BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > - will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > - will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # Failed test 'use Bio::Annotation::TagTree;' > # at t/Annotation/Annotation.t line 20. > # Tried to use 'Bio::Annotation::TagTree'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # Failed test 'default itext' > # at t/Annotation/Annotation.t line 307. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > > # Failed test 'itext' > # at t/Annotation/Annotation.t line 315. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > 1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > 8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > Failed 17/19 tests, 10.53% okay > 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 > 11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > 9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > 19/267 skipped: various reasons > 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 > 10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > 10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > 4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > 14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > 13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > 10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > 10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > 8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > 3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > 2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > all 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.............................ok 1/1093 > # Failed (TODO) test at t/SearchIO/blast.t line 527. > # '0.852' > # > > # '0.9' > > # Failed (TODO) test at t/SearchIO/blast.t line 528. > # '1.599' > # <= > # '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # got: '0.946' > # expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # got: undef > # expected: '31984247' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # got: undef > # expected: '88780' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # got: undef > # expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > 4/45 skipped: various reasons > 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...........................ok 1/116 > # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # expected: undef > > # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # got: '\-\.=~' > # expected: '-\?' > > # Failed (TODO) test at t/Seq/LocatableSeq.t 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 > all 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 > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > 7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > all 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..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # Failed test 'use Bio::SeqIO::chaos;' > # at t/SeqIO/chaos.t line 15. > # Tried to use 'Bio::SeqIO::chaos'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > all 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 > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # Failed (TODO) test 'primary_id' > # at t/SeqIO/gcg.t line 54. > # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > all 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 > all 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 > all 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..................................ok 1/59 > # Failed (TODO) test 'accuracies' > # at t/SeqIO/scf.t line 78. > # got: 'ARRAY(0x100ac5648)' > # expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # Failed test 'use Bio::SeqIO::swiss;' > # at t/SeqIO/swiss.t line 12. > # Tried to use 'Bio::SeqIO::swiss'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > 112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # at t/SeqTools/GuessSeqFormat.t line 71. > # got: '0' > # expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > 5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > all 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 > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > 12/16 skipped: various reasons > 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 > all 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......................skipped > all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > 12/45 skipped: various reasons > 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 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 > all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > 2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > 3/4 skipped: various reasons > 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 > 15/26 skipped: various reasons > Failed Test Stat Wstat Total Fail List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t 255 65280 28 42 8-28 > t/AlignIO/arp.t 255 65280 48 92 3-48 > t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 > t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 > t/LocalDB/Flat.t 255 65280 24 20 15-24 > t/LocalDB/Index.t 255 65280 64 66 32-64 > t/SeqIO/Handler.t 255 65280 550 1098 2-550 > t/SeqIO/chaos.t 1 256 8 1 1 > t/SeqIO/swiss.t 255 65280 240 479 1-240 > t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 > t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From wkretzsch at gmail.com Fri Jul 30 11:37:08 2010 From: wkretzsch at gmail.com (Warren W. Kretzschmar) Date: Fri, 30 Jul 2010 11:37:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Alternatively I think you might have run "make install" when what you actually wanted to run was "sudo make install". The sudo means you install everything with root rights (which you say you have). It'll ask you for a password and then it will have the rights to install into /usr/local/bin Cheers, Warren On Fri, Jul 30, 2010 at 9:54 AM, Robson de Souza wrote: > Did you try, as root, > > ./Build.pl --install_base /opt/local > > ? > > Also, check the INSTALL file at the root of the bioperl distribution. > Robson > > On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: >> Hi there >> I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. >> I am not able to complete the installation as every time I get: >> >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> ?I have tried using both methods to install into a local folder and get the same thing >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/home/users/carrieomalley/bin' >> mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. >> >> >> If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( >> >> >> Many thanks in advance >> Carrie >> >> >> >> >> >> Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL >> Checking whether your kit is complete... >> Looks good >> >> Checking prerequisites... >> ?- ERROR: Data::Stag is not installed >> (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) >> CPAN: Storable loaded ok (v2.18) >> Going to read /Users/carrieomalley/.cpan/Metadata >> ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT >> Running install for module 'Data::Stag' >> 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' >> Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok >> x Data-Stag-0.11/ >> x Data-Stag-0.11/c-ext/ >> x Data-Stag-0.11/c-ext/README.c-ext >> x Data-Stag-0.11/c-ext/staglib.c >> x Data-Stag-0.11/c-ext/staglib.h >> x Data-Stag-0.11/Changes >> x Data-Stag-0.11/Data/ >> x Data-Stag-0.11/Data/Stag/ >> x Data-Stag-0.11/Data/Stag/Arr2HTML.pm >> x Data-Stag-0.11/Data/Stag/Base.pm >> x Data-Stag-0.11/Data/Stag/BaseGenerator.pm >> x Data-Stag-0.11/Data/Stag/BaseHandler.pm >> x Data-Stag-0.11/Data/Stag/ChainHandler.pm >> x Data-Stag-0.11/Data/Stag/DTDWriter.pm >> x Data-Stag-0.11/Data/Stag/GraphHandler.pm >> x Data-Stag-0.11/Data/Stag/HashDB.pm >> x Data-Stag-0.11/Data/Stag/IndentParser.pm >> x Data-Stag-0.11/Data/Stag/IndentWriter.pm >> x Data-Stag-0.11/Data/Stag/ITextParser.pm >> x Data-Stag-0.11/Data/Stag/ITextWriter.pm >> x Data-Stag-0.11/Data/Stag/null.pm >> x Data-Stag-0.11/Data/Stag/PerlWriter.pm >> x Data-Stag-0.11/Data/Stag/PodParser.pm >> x Data-Stag-0.11/Data/Stag/SAX2Stag.pm >> x Data-Stag-0.11/Data/Stag/Simple.pm >> x Data-Stag-0.11/Data/Stag/StagDB.pm >> x Data-Stag-0.11/Data/Stag/StagI.pm >> x Data-Stag-0.11/Data/Stag/StagImpl.pm >> x Data-Stag-0.11/Data/Stag/SxprParser.pm >> x Data-Stag-0.11/Data/Stag/SxprWriter.pm >> x Data-Stag-0.11/Data/Stag/Util.pm >> x Data-Stag-0.11/Data/Stag/Writer.pm >> x Data-Stag-0.11/Data/Stag/XMLParser.pm >> x Data-Stag-0.11/Data/Stag/XMLWriter.pm >> x Data-Stag-0.11/Data/Stag/XSLHandler.pm >> x Data-Stag-0.11/Data/Stag/XSLTHandler.pm >> x Data-Stag-0.11/Data/Stag.pm >> x Data-Stag-0.11/dev/ >> x Data-Stag-0.11/dev/create-manifest.sh >> x Data-Stag-0.11/dev/data-stag.spec >> x Data-Stag-0.11/dev/mkspec.pl >> x Data-Stag-0.11/elisp/ >> x Data-Stag-0.11/elisp/itext-mode.el >> x Data-Stag-0.11/homepage/ >> x Data-Stag-0.11/homepage/archBIG.png >> x Data-Stag-0.11/homepage/dbstag-tutorial.sgml >> x Data-Stag-0.11/homepage/images/ >> x Data-Stag-0.11/homepage/images/k-schema-diagram.png >> x Data-Stag-0.11/homepage/images/rr-schema-diagram.png >> x Data-Stag-0.11/homepage/index.html >> x Data-Stag-0.11/homepage/makefile >> x Data-Stag-0.11/homepage/mk.sh >> x Data-Stag-0.11/homepage/mkpodhtml.pl >> x Data-Stag-0.11/homepage/mkscriptdoc.pl >> x Data-Stag-0.11/homepage/script-docs/ >> x Data-Stag-0.11/homepage/script-docs/selectall_html.html >> x Data-Stag-0.11/homepage/script-docs/selectall_xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html >> x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html >> x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html >> x Data-Stag-0.11/homepage/script-docs/stag-db.html >> x Data-Stag-0.11/homepage/script-docs/stag-diff.html >> x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-elcount.html >> x Data-Stag-0.11/homepage/script-docs/stag-eval.html >> x Data-Stag-0.11/homepage/script-docs/stag-filter.html >> x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-flatten.html >> x Data-Stag-0.11/homepage/script-docs/stag-grep.html >> x Data-Stag-0.11/homepage/script-docs/stag-handle.html >> x Data-Stag-0.11/homepage/script-docs/stag-ir.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-join.html >> x Data-Stag-0.11/homepage/script-docs/stag-merge.html >> x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html >> x Data-Stag-0.11/homepage/script-docs/stag-parse.html >> x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html >> x Data-Stag-0.11/homepage/script-docs/stag-query.html >> x Data-Stag-0.11/homepage/script-docs/stag-show-template.html >> x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html >> x Data-Stag-0.11/homepage/script-docs/stag-splitter.html >> x Data-Stag-0.11/homepage/script-docs/stag-storenode.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html >> x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html >> x Data-Stag-0.11/homepage/script-docs/stag-view.html >> x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html >> x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html >> x Data-Stag-0.11/homepage/script-list.html >> x Data-Stag-0.11/homepage/stag-db-tutorial.html >> x Data-Stag-0.11/homepage/stag-poster.html >> x Data-Stag-0.11/INSTALL >> x Data-Stag-0.11/Makefile.PL >> x Data-Stag-0.11/MANIFEST >> x Data-Stag-0.11/META.yml >> x Data-Stag-0.11/README >> x Data-Stag-0.11/scripts/ >> x Data-Stag-0.11/scripts/stag-autoschema.pl >> x Data-Stag-0.11/scripts/stag-db.pl >> x Data-Stag-0.11/scripts/stag-diff.pl >> x Data-Stag-0.11/scripts/stag-drawtree.pl >> x Data-Stag-0.11/scripts/stag-elcount.pl >> x Data-Stag-0.11/scripts/stag-eval.pl >> x Data-Stag-0.11/scripts/stag-filter.pl >> x Data-Stag-0.11/scripts/stag-findsubtree.pl >> x Data-Stag-0.11/scripts/stag-flatten.pl >> x Data-Stag-0.11/scripts/stag-grep.pl >> x Data-Stag-0.11/scripts/stag-handle.pl >> x Data-Stag-0.11/scripts/stag-itext2simple.pl >> x Data-Stag-0.11/scripts/stag-itext2sxpr.pl >> x Data-Stag-0.11/scripts/stag-itext2xml.pl >> x Data-Stag-0.11/scripts/stag-join.pl >> x Data-Stag-0.11/scripts/stag-merge.pl >> x Data-Stag-0.11/scripts/stag-mogrify.pl >> x Data-Stag-0.11/scripts/stag-parse.pl >> x Data-Stag-0.11/scripts/stag-query.pl >> x Data-Stag-0.11/scripts/stag-splitter.pl >> x Data-Stag-0.11/scripts/stag-view.pl >> x Data-Stag-0.11/scripts/stag-xml2itext.pl >> x Data-Stag-0.11/scripts/stag-xmlsplit.pl >> x Data-Stag-0.11/t/ >> x Data-Stag-0.11/t/animal.x >> x Data-Stag-0.11/t/autoschema.t >> x Data-Stag-0.11/t/barfly.x >> x Data-Stag-0.11/t/bio.x >> x Data-Stag-0.11/t/chainhandler.t >> x Data-Stag-0.11/t/collapse.x >> x Data-Stag-0.11/t/data/ >> x Data-Stag-0.11/t/data/attrs.xml >> x Data-Stag-0.11/t/data/bf.txt >> x Data-Stag-0.11/t/data/eco.el >> x Data-Stag-0.11/t/data/eco.itext >> x Data-Stag-0.11/t/data/homol.itext >> x Data-Stag-0.11/t/data/persons.el >> x Data-Stag-0.11/t/db.t >> x Data-Stag-0.11/t/emptytag.t >> x Data-Stag-0.11/t/get.t >> x Data-Stag-0.11/t/graph.x >> x Data-Stag-0.11/t/handlers.t >> x Data-Stag-0.11/t/handlers2.t >> x Data-Stag-0.11/t/handlers2.x >> x Data-Stag-0.11/t/hashdb.t >> x Data-Stag-0.11/t/hashdb.x >> x Data-Stag-0.11/t/homol.t >> x Data-Stag-0.11/t/lisp.x >> x Data-Stag-0.11/t/parsestr.t >> x Data-Stag-0.11/t/path.x >> x Data-Stag-0.11/t/path2.x >> x Data-Stag-0.11/t/qmatch.t >> x Data-Stag-0.11/t/roundtrip-attrs.t >> x Data-Stag-0.11/t/set-attrs.t >> x Data-Stag-0.11/t/set.t >> x Data-Stag-0.11/t/sxpr.t >> x Data-Stag-0.11/t/unhash.t >> x Data-Stag-0.11/t/unset.t >> x Data-Stag-0.11/t/write.t >> x Data-Stag-0.11/t/xml1.t >> x Data-Stag-0.11/t/xml2.t >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> >> >> External Module XML::LibXSLT, XSLT, >> ?is not installed on this computer. >> ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations >> >> External Module XML::Parser::PerlSAX, SAX Handler, >> ?is not installed on this computer. >> ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML >> >> External Module GD, Graphical Drawing Toolkit, >> ?is not installed on this computer. >> ?stag-drawtree.pl in Data::Stag needs it for drawing trees >> >> External Module Graph::Directed, Generic Graph data stucture and algorithms, >> ?is not installed on this computer. >> ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs >> >> External Module Tk, Tk, >> ?is not installed on this computer. >> ?stag-view.pl in Data::Stag needs it for tree viewer >> >> >> Information: >> >> ? There are some external packages and perl modules, listed above, which >> ? stag uses. This only effects the functionality which is listed above: >> ? the rest of stag will work fine, which includes nearly all of the >> ? core functionality. >> >> ? Enjoy the rest of stag, which you can use after going 'make install' >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Data >> Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites >> cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm >> cp Data/Stag.pm blib/lib/Data/Stag.pm >> cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm >> cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm >> cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm >> cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm >> cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm >> cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm >> cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm >> cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm >> cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm >> cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm >> cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm >> cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm >> cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm >> cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm >> cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm >> cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm >> cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm >> cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm >> cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm >> cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm >> cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm >> cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm >> cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm >> cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm >> cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm >> cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm >> cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm >> cp scripts/stag-view.pl blib/script/stag-view.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl >> cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl >> cp scripts/stag-grep.pl blib/script/stag-grep.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl >> cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl >> cp scripts/stag-merge.pl blib/script/stag-merge.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl >> cp scripts/stag-parse.pl blib/script/stag-parse.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl >> cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl >> cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl >> cp scripts/stag-join.pl blib/script/stag-join.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl >> cp scripts/stag-db.pl blib/script/stag-db.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl >> cp scripts/stag-filter.pl blib/script/stag-filter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl >> cp scripts/stag-handle.pl blib/script/stag-handle.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl >> cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl >> cp scripts/stag-query.pl blib/script/stag-query.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl >> cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl >> cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl >> cp scripts/stag-flatten.pl blib/script/stag-flatten.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl >> cp scripts/stag-splitter.pl blib/script/stag-splitter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl >> cp scripts/stag-diff.pl blib/script/stag-diff.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl >> cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl >> Manifying blib/man1/stag-view.pl.1 >> Manifying blib/man1/stag-mogrify.pl.1 >> Manifying blib/man1/stag-grep.pl.1 >> Manifying blib/man1/stag-handle.pl.1 >> Manifying blib/man1/stag-drawtree.pl.1 >> Manifying blib/man1/stag-query.pl.1 >> Manifying blib/man1/stag-merge.pl.1 >> Manifying blib/man1/stag-parse.pl.1 >> Manifying blib/man1/stag-findsubtree.pl.1 >> Manifying blib/man1/stag-join.pl.1 >> Manifying blib/man1/stag-autoschema.pl.1 >> Manifying blib/man1/stag-db.pl.1 >> Manifying blib/man1/stag-flatten.pl.1 >> Manifying blib/man1/stag-splitter.pl.1 >> Manifying blib/man1/stag-diff.pl.1 >> Manifying blib/man1/stag-filter.pl.1 >> Manifying blib/man3/Data::Stag::StagDB.3pm >> Manifying blib/man3/Data::Stag::SxprWriter.3pm >> Manifying blib/man3/Data::Stag.3pm >> Manifying blib/man3/Data::Stag::ChainHandler.3pm >> Manifying blib/man3/Data::Stag::IndentParser.3pm >> Manifying blib/man3/Data::Stag::Simple.3pm >> Manifying blib/man3/Data::Stag::SAX2Stag.3pm >> Manifying blib/man3/Data::Stag::Arr2HTML.3pm >> Manifying blib/man3/Data::Stag::XSLHandler.3pm >> Manifying blib/man3/Data::Stag::PerlWriter.3pm >> Manifying blib/man3/Data::Stag::XSLTHandler.3pm >> Manifying blib/man3/Data::Stag::DTDWriter.3pm >> Manifying blib/man3/Data::Stag::Writer.3pm >> Manifying blib/man3/Data::Stag::XMLWriter.3pm >> Manifying blib/man3/Data::Stag::GraphHandler.3pm >> Manifying blib/man3/Data::Stag::XMLParser.3pm >> Manifying blib/man3/Data::Stag::StagImpl.3pm >> Manifying blib/man3/Data::Stag::PodParser.3pm >> Manifying blib/man3/Data::Stag::BaseGenerator.3pm >> Manifying blib/man3/Data::Stag::IndentWriter.3pm >> Manifying blib/man3/Data::Stag::HashDB.3pm >> Manifying blib/man3/Data::Stag::null.3pm >> Manifying blib/man3/Data::Stag::ITextParser.3pm >> Manifying blib/man3/Data::Stag::BaseHandler.3pm >> Manifying blib/man3/Data::Stag::ITextWriter.3pm >> Manifying blib/man3/Data::Stag::SxprParser.3pm >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/autoschema.........ok >> t/chainhandler.......ok >> t/db.................ok >> t/emptytag...........ok >> ? ? ? ?3/3 skipped: various reasons >> t/get................ok >> t/handlers...........ok >> t/handlers2..........ok >> ? ? ? ?1/9 skipped: various reasons >> t/hashdb.............ok >> t/homol..............ok >> t/parsestr...........ok >> ? ? ? ?6/6 skipped: various reasons >> t/qmatch.............ok >> t/roundtrip-attrs....ok >> ? ? ? ?5/5 skipped: various reasons >> t/set-attrs..........ok >> ? ? ? ?3/3 skipped: various reasons >> t/set................ok >> t/sxpr...............ok >> t/unhash.............ok >> t/unset..............ok >> t/write..............ok >> t/xml1...............ok >> ? ? ? ?7/7 skipped: various reasons >> t/xml2...............ok >> ? ? ? ?4/4 skipped: various reasons >> All tests successful, 29 subtests skipped. >> Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make test -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make install >> Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at -e line 1 >> make: *** [pure_site_install] Error 13 >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make install ?-- NOT OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> >> *** (back in Bioperl Build.PL) *** >> Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n >> ?- ERROR: You chose to install Data::Stag but it failed to install >> ?* Optional prerequisite Ace is not installed >> ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) >> ?* Optional prerequisite Spreadsheet::ParseExcel is not installed >> ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) >> ?* Optional prerequisite Math::Random is not installed >> ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) >> ?* Optional prerequisite Graph is not installed >> ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) >> ?* Optional prerequisite SVG::Graph is not installed >> ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) >> ?* Optional prerequisite SOAP::Lite is not installed >> ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) >> ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed >> ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) >> ?* Optional prerequisite GraphViz is not installed >> ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) >> ?* Optional prerequisite Array::Compare is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite Convert::Binary::C is not installed >> ? (wanted for strider functionality, used by Bio::SeqIO::strider) >> ?* Optional prerequisite Algorithm::Munkres is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite XML::Twig is not installed >> ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) >> ?* Optional prerequisite Set::Scalar is not installed >> ? (wanted for proper operation, used by Bio::Tree::Compatible) >> ?* Optional prerequisite XML::Parser::PerlSAX is not installed >> ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) >> ?* Optional prerequisite XML::SAX::Writer is not installed >> ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) >> ?* Optional prerequisite Clone is not installed >> ? (wanted for cloning objects, used by Bio::Tools::Primer3) >> ?* Optional prerequisite XML::DOM::XPath is not installed >> ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) >> ?* Optional prerequisite PostScript::TextBlock is not installed >> ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions >> of the modules indicated above before proceeding with this installation >> >> Checking features: >> ?BioDBGFF.................disabled >> ? ?* MySQL, Pg nor Oracle DBI drivers are installed >> ?BioDBSeqFeature_mysql....disabled >> ? ?- DBD::mysql is not installed >> ?Network..................enabled >> ?BioDBSeqFeature_BDB......enabled >> >> Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] >> ?- will install all scripts >> >> Do you want to run tests that require connection to servers across the internet >> (likely to cause some failures)? y/n [n] n >> ?- will not run internet-requiring tests >> Deleting Build >> Removed previous script 'Build' >> >> Creating new 'Build' script for 'BioPerl' version '1.006000' >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> t/Align/AlignStats...........................ok >> t/Align/AlignUtil............................ok >> t/Align/SimpleAlign..........................ok >> t/Align/TreeBuild............................ok >> t/Align/Utilities............................ok >> t/AlignIO/AlignIO............................ok 1/28 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> # Looks like you planned 28 tests but only ran 7. >> # Looks like your test died just after 7. >> t/AlignIO/AlignIO............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 8-28 >> ? ? ? ?Failed 21/28 tests, 25.00% okay >> t/AlignIO/arp................................ok 1/48 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> # Looks like you planned 48 tests but only ran 2. >> # Looks like your test died just after 2. >> t/AlignIO/arp................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-48 >> ? ? ? ?Failed 46/48 tests, 4.17% okay >> 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......................ok 1/159 >> # ? Failed test 'use Bio::Annotation::TagTree;' >> # ? at t/Annotation/Annotation.t line 20. >> # ? ? Tried to use 'Bio::Annotation::TagTree'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. >> # Compilation failed in require at (eval 37) line 2. >> # BEGIN failed--compilation aborted at (eval 37) line 2. >> t/Annotation/Annotation......................NOK 9/159 >> # ? Failed test 'default itext' >> # ? at t/Annotation/Annotation.t line 307. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> >> # ? Failed test 'itext' >> # ? at t/Annotation/Annotation.t line 315. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. >> # Looks like you planned 159 tests but only ran 119. >> # Looks like you failed 3 tests of 119 run. >> # Looks like your test died just after 119. >> t/Annotation/Annotation......................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 9, 117, 119-159 >> ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) >> t/Annotation/AnnotationAdaptor...............ok >> t/Assembly/Assembly..........................ok 1/51 >> # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. >> t/Assembly/Assembly..........................ok >> t/Assembly/ContigSpectrum....................ok >> t/Biblio/Biblio..............................ok >> ? ? ? ?1/24 skipped: various reasons >> t/Biblio/References..........................ok >> t/Biblio/biofetch............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Biblio/eutils..............................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/ClusterIO/ClusterIO........................ok >> ? ? ? ?8/12 skipped: various reasons >> t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/ClusterIO/SequenceFamily.t:16 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. >> # Looks like you planned 19 tests but only ran 2. >> # Looks like your test died just after 2. >> t/ClusterIO/SequenceFamily...................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-19 >> ? ? ? ?Failed 17/19 tests, 10.53% okay >> 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 >> ? ? ? ?11/279 skipped: various reasons >> t/LocalDB/BlastIndex.........................ok >> t/LocalDB/DBFasta............................ok >> t/LocalDB/DBQual.............................ok >> t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 >> STACK: t/LocalDB/Flat.t:89 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. >> # Looks like you planned 24 tests but only ran 14. >> # Looks like your test died just after 14. >> t/LocalDB/Flat...............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-24 >> ? ? ? ?Failed 10/24 tests, 58.33% okay >> t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 >> STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 >> STACK: t/LocalDB/Index.t:91 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. >> # Looks like you planned 64 tests but only ran 31. >> # Looks like your test died just after 31. >> t/LocalDB/Index..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 32-64 >> ? ? ? ?Failed 33/64 tests, 48.44% okay >> t/LocalDB/Registry...........................ok >> ? ? ? ?9/14 skipped: various reasons >> t/LocalDB/SeqFeature.........................ok >> t/LocalDB/transfac_pro.......................ok >> t/Map/Cyto...................................ok >> t/Map/Linkage................................ok >> t/Map/Map....................................ok >> ? ? ? ?19/267 skipped: various reasons >> 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 >> ? ? ? ?10/14 skipped: various reasons >> t/Matrix/SiteMatrix..........................ok >> t/Ontology/GOterm............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/GraphAdaptor......................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/go.............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/interpro.......................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/Ontology/IO/obo............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Ontology..........................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/OntologyEngine....................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/OntologyStore.....................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Relationship......................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/RelationshipType..................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/Term..............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Perl.......................................ok >> ? ? ? ?10/29 skipped: various reasons >> 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..................................ok >> t/PopGen/Coalescent..........................ok >> t/PopGen/HtSNP...............................ok >> t/PopGen/MK..................................ok >> ? ? ? ?4/46 skipped: various reasons >> t/PopGen/PopGen..............................ok >> t/PopGen/PopGenSims..........................ok >> t/PopGen/TagHaplotype........................ok >> t/RemoteDB/BioFetch..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/CUTG..............................ok >> ? ? ? ?14/37 skipped: various reasons >> t/RemoteDB/DB................................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EMBL..............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EUtilities........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/HIV/HIV...........................ok >> ? ? ? ?13/30 skipped: various reasons >> t/RemoteDB/HIV/HIVAnnotProcessor.............ok >> t/RemoteDB/HIV/HIVQuery......................ok >> ? ? ? ?10/41 skipped: various reasons >> t/RemoteDB/HIV/HIVQueryHelper................ok >> t/RemoteDB/RefSeq............................ok >> ? ? ? ?10/16 skipped: various reasons >> t/RemoteDB/SeqHound..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqRead_fail......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqVersion........................ok >> ? ? ? ?8/10 skipped: various reasons >> t/RemoteDB/Taxonomy..........................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/Restriction/Analysis.......................ok >> t/Restriction/Gel............................ok >> t/Restriction/IO.............................ok 1/18 >> # ? Failed (TODO) test at t/Restriction/IO.t line 31. >> t/Restriction/IO.............................ok >> ? ? ? ?3/18 skipped: various reasons >> t/Root/Exception.............................ok >> t/Root/RootI.................................ok >> t/Root/RootIO................................ok >> ? ? ? ?2/31 skipped: various reasons >> t/Root/Storable..............................ok >> t/Root/Tempfile..............................ok >> t/Root/Utilities.............................ok >> t/SearchDist.................................skipped >> ? ? ? ?all 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.............................ok 1/1093 >> # ? Failed (TODO) test at t/SearchIO/blast.t line 527. >> # ? ? '0.852' >> # ? ? ? ? > >> # ? ? '0.9' >> >> # ? Failed (TODO) test at t/SearchIO/blast.t line 528. >> # ? ? '1.599' >> # ? ? ? ? <= >> # ? ? '1' >> t/SearchIO/blast.............................ok >> t/SearchIO/blast_pull........................ok 1/289 >> # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. >> # ? ? ? ? ?got: '0.946' >> # ? ? expected: '0.943' >> t/SearchIO/blast_pull........................ok >> t/SearchIO/blasttable........................ok >> t/SearchIO/blastxml..........................ok 1/298 >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. >> # ? ? ? ? ?got: undef >> # ? ? expected: '31984247' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. >> # ? ? ? ? ?got: undef >> # ? ? expected: '88780' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. >> # ? ? ? ? ?got: undef >> # ? ? expected: '49' >> t/SearchIO/blastxml..........................ok >> t/SearchIO/cross_match.......................ok >> t/SearchIO/erpin.............................ok >> t/SearchIO/exonerate.........................ok >> ? ? ? ?4/45 skipped: various reasons >> 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...........................ok 1/116 >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. >> # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' >> # ? ? expected: undef >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. >> # ? ? ? ? ?got: '\-\.=~' >> # ? ? expected: '-\?' >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature......................ok >> ? ? ? ?7/214 skipped: various reasons >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> t/SeqIO......................................ok >> t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. >> BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqIO/Handler.t:20 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. >> # Looks like you planned 550 tests but only ran 1. >> # Looks like your test died just after 1. >> t/SeqIO/Handler..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 2-550 >> ? ? ? ?Failed 549/550 tests, 0.18% okay >> t/SeqIO/MultiFile............................ok >> t/SeqIO/Multiple_fasta.......................ok >> t/SeqIO/SeqBuilder...........................ok >> t/SeqIO/Splicedseq...........................ok >> t/SeqIO/abi..................................skipped >> ? ? ? ?all 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..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/asciitree............................ok >> t/SeqIO/bsml.................................skipped >> ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed >> t/SeqIO/bsml_sax.............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/chadoxml.............................ok >> t/SeqIO/chaos................................ >> # ? Failed test 'use Bio::SeqIO::chaos;' >> # ? at t/SeqIO/chaos.t line 15. >> # ? ? Tried to use 'Bio::SeqIO::chaos'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. >> # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> # Looks like you failed 1 test of 8. >> t/SeqIO/chaos................................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED test 1 >> ? ? ? ?Failed 1/8 tests, 87.50% okay >> t/SeqIO/chaosxml.............................skipped >> ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed >> t/SeqIO/ctf..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/embl.................................ok >> t/SeqIO/entrezgene...........................skipped >> ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed >> t/SeqIO/excel................................skipped >> ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed >> t/SeqIO/exp..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/gcg..................................ok 1/17 >> # ? Failed (TODO) test 'primary_id' >> # ? at t/SeqIO/gcg.t line 54. >> # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' >> # ? ? expected: 'roa1_drome' >> t/SeqIO/gcg..................................ok >> t/SeqIO/genbank..............................ok >> t/SeqIO/interpro.............................skipped >> ? ? ? ?all 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 >> ? ? ? ?all 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 >> ? ? ? ?all 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..................................ok 1/59 >> # ? Failed (TODO) test 'accuracies' >> # ? at t/SeqIO/scf.t line 78. >> # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' >> # ? ? expected: '482' >> t/SeqIO/scf..................................ok >> t/SeqIO/strider..............................skipped >> ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed >> t/SeqIO/swiss................................ >> # ? Failed test 'use Bio::SeqIO::swiss;' >> # ? at t/SeqIO/swiss.t line 12. >> # ? ? Tried to use 'Bio::SeqIO::swiss'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. >> # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. >> # Looks like you planned 240 tests but only ran 1. >> # Looks like you failed 1 test of 1 run. >> # Looks like your test died just after 1. >> t/SeqIO/swiss................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-240 >> ? ? ? ?Failed 240/240 tests, 0.00% okay >> t/SeqIO/tab..................................ok >> t/SeqIO/table................................ok >> ? ? ? ?112/450 skipped: various reasons >> t/SeqIO/tigr.................................ok >> t/SeqIO/tigrxml..............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/tinyseq..............................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/ztr..................................skipped >> ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqTools/GuessSeqFormat.t:62 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> t/SeqTools/GuessSeqFormat....................NOK 25/49 >> # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. >> # ' >> # ? at t/SeqTools/GuessSeqFormat.t line 71. >> # ? ? ? ? ?got: '0' >> # ? ? expected: '1' >> # Looks like you planned 49 tests but ran 1 extra. >> # Looks like you failed 1 test of 50 run. >> t/SeqTools/GuessSeqFormat....................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED tests 25, 50 >> ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) >> t/SeqTools/OddCodes..........................ok >> t/SeqTools/SeqPattern........................ok >> t/SeqTools/SeqStats..........................ok >> t/SeqTools/SeqUtils..........................ok >> t/SeqTools/SeqWords..........................ok >> t/Species....................................ok >> ? ? ? ?5/21 skipped: various reasons >> t/Structure/IO...............................ok >> t/Structure/Structure........................ok >> t/Symbol.....................................ok >> t/TaxonTree..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Domcut..............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/ELM.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/GOR4................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/HNN.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Mitoprot............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/NetPhos.............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/Tools/Analysis/Protein/Scansite.t:23 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. >> # Looks like you planned 14 tests but only ran 4. >> # Looks like your test died just after 4. >> t/Tools/Analysis/Protein/Scansite............dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 5-14 >> ? ? ? ?Failed 10/14 tests, 28.57% okay >> t/Tools/Analysis/Protein/Sopma...............ok >> ? ? ? ?12/16 skipped: various reasons >> 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 >> ? ? ? ?all 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......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Run/StandAloneBlast..................ok >> ? ? ? ?12/45 skipped: various reasons >> 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 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 >> ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed >> t/Tree/Node..................................ok >> t/Tree/PhyloNetwork/Factory..................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/GraphViz.................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/MuVector.................ok >> t/Tree/PhyloNetwork/PhyloNetwork.............skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/RandomFactory............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/TreeFactory..............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/RandomTreeFactory.....................ok >> t/Tree/Tree..................................ok >> t/Tree/TreeIO................................ok >> ? ? ? ?2/74 skipped: various reasons >> t/Tree/TreeIO/lintree........................ok >> t/Tree/TreeIO/newick.........................ok >> t/Tree/TreeIO/nexus..........................ok >> t/Tree/TreeIO/nhx............................ok >> t/Tree/TreeIO/phyloxml.......................ok >> t/Tree/TreeIO/svggraph.......................ok >> ? ? ? ?3/4 skipped: various reasons >> 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 >> ? ? ? ?15/26 skipped: various reasons >> Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed >> ------------------------------------------------------------------------------- >> t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 >> t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 >> t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 >> t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 >> t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 >> t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 >> t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 >> t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 >> t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 >> t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 >> t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 >> 57 tests and 313 subtests skipped. >> Failed 11/318 test scripts. 970/17228 subtests failed. >> Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) >> Failed 11/318 test programs. 970/17228 subtests failed. >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 >> Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 >> Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 >> Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 >> Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 >> Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 >> Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 >> Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 >> Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 >> Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 >> Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 >> Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 >> Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 >> Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 >> Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 >> Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 >> Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 >> Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 >> Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 >> Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 >> Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 >> Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 >> Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 >> Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 >> Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 >> Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 >> Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 >> Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 >> Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 >> Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 >> Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 >> Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 >> Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 >> Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 >> Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 >> Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 >> Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 >> Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 >> Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 >> Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 >> Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 >> Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 >> Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 >> Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 >> Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 >> Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 >> Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 >> Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 >> Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 >> Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 >> Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 >> Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 >> Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 >> Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 >> Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 >> Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 >> Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 sdshlxh at gmail.com Fri Jul 30 13:14:23 2010 From: sdshlxh at gmail.com (Ping Yao) Date: Fri, 30 Jul 2010 12:14:23 -0500 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: please remove me from the list. From Kevin.M.Brown at asu.edu Fri Jul 30 13:29:25 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Fri, 30 Jul 2010 10:29:25 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: <1A4207F8295607498283FE9E93B775B406D682E2@EX02.asurite.ad.asu.edu> You can remove yourself by following the link at the bottom of every email. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ping Yao Sent: Friday, July 30, 2010 10:14 AM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 please remove me from the list. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Sat Jul 31 16:56:49 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sat, 31 Jul 2010 16:56:49 -0400 Subject: [Bioperl-l] SOAP Eutilities Message-ID: Hi, Bio::DB::SoapEUtilities, referred in the HOWTO on EUtilities, seems to have disappeared from the Git repository. A simple git clone git://github.com/bioperl/bioperl-live.git does not download it. Any ideas why? Robson From twaddlac at gmail.com Thu Jul 1 10:45:01 2010 From: twaddlac at gmail.com (twaddlac) Date: Thu, 1 Jul 2010 07:45:01 -0700 (PDT) Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? Message-ID: <29046535.post@talk.nabble.com> Hi, I am having a bit of trouble reading in a qual file; I would like to input the qual file into a hash but I can't seem to find a method that returns the qual sequence. Any ideas? Thank you in advance! -- View this message in context: http://old.nabble.com/Read-in-a-Qual-File-like-a-Fasta--tp29046535p29046535.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From rmb32 at cornell.edu Thu Jul 1 20:18:58 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 01 Jul 2010 17:18:58 -0700 Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? In-Reply-To: <29046535.post@talk.nabble.com> References: <29046535.post@talk.nabble.com> Message-ID: <4C2D3072.6080803@cornell.edu> You probably want to do something like: use Bio::SeqIO; my $qual_in = Bio::SeqIO->new( -format => 'qual', -file => $ARGV[0], ); while( my $q = $qual_in->next_seq ) { print "qual for ".$q->id." is: "; print "$_ " for @{ $q->qual }; print "\n"; } twaddlac wrote: > Hi, > > I am having a bit of trouble reading in a qual file; I would like to > input the qual file into a hash but I can't seem to find a method that > returns the qual sequence. Any ideas? Thank you in advance! From cjfields at illinois.edu Fri Jul 2 09:48:19 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 08:48:19 -0500 Subject: [Bioperl-l] BioPerl Switching to GitHub Organization Message-ID: <50D544D2-5F49-482F-9E7F-EB462871B380@illinois.edu> GitHub (as expected) just released their setup for organizations, including open-source projects. The announcement is here: http://github.com/blog/674-introducing-organizations I have already moved bioperl over to an organization account and have added a few co-owners of the github repository. The move is transparent, no one should notice any difference in checking out code. I'm working on reassigning teams to projects at this time, so please post here if there are any problems. chris From iatropoul at gmail.com Fri Jul 2 00:21:09 2010 From: iatropoul at gmail.com (George Iatropoulos) Date: Thu, 1 Jul 2010 21:21:09 -0700 (PDT) Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) Message-ID: Hi guys! I'd like to thank you for this important project. I currently develop a script that uses the SeqIO module to read fasta or files with other bio-formats. However your installation instructions are too difficult to be followed, or even outdated, especially for the mac platform. After trying a week I really can't install bioperl on a Snow Leopard machine (perl 5.10.0) and I tried the CPAN and the fink method. None of them works! Especially cpan seems to mess up with itself and now doesn't install anything! As for the ubuntu platform a simple command like: "sudo apt-get install bioperl" simply does the trick! However I couldn't find this simple command in your installation guidelines, and I don't really understand why I should set up a server, before installing bioperl and then follow this complicated series of instructions, to achieve something that is so simple! I understand that you try to give complete instructions for people who may be pleased with more advanced stuff, but please don't forget biology students who don't have a deep computational background. These guys like me would appreciate some simple stuff to get their job and their projects done, without needing to waste days to figure out complicated-guru stuff. Best wishes and many thanks to all of you because bioperl is really important for us! Georgios Iatropoulos From cjfields at illinois.edu Fri Jul 2 11:46:46 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 10:46:46 -0500 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: References: Message-ID: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > Hi guys! > > I'd like to thank you for this important project. I currently develop > a script that uses the SeqIO module to read fasta or files with other > bio-formats. However your installation instructions are too difficult > to be followed, or even outdated, especially for the mac platform. > > After trying a week I really can't install bioperl on a Snow Leopard > machine (perl 5.10.0) and I tried the CPAN and the fink method. None > of them works! Especially cpan seems to mess up with itself and now > doesn't install anything! That's odd. Can you send me what you are seeing? > As for the ubuntu platform a simple command like: "sudo apt-get > install bioperl" simply does the trick! > However I couldn't find this simple command in your installation > guidelines, and I don't really understand why I should set up a > server, before installing bioperl and then follow this complicated > series of instructions, to achieve something that is so simple! That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > I understand that you try to give complete instructions for people who > may be pleased with more advanced stuff, but please don't forget > biology students who don't have a deep computational background. These > guys like me would appreciate some simple stuff to get their job and > their projects done, without needing to waste days to figure out > complicated-guru stuff. We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > Best wishes and many thanks to all of you because bioperl is really > important for us! > > Georgios Iatropoulos Sorry for the troubles, and thanks for letting us know. Any additional details about installation problems are very welcome. Also, the installation page on the bioperl website is editable (it is a wiki :). So, feel free to add more detail where needed, or use the discussion page to point out problems. chris From steffen_moeller at gmx.de Fri Jul 2 12:39:00 2010 From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=) Date: Fri, 02 Jul 2010 18:39:00 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <4C2E1624.2070402@gmx.de> Hello, On 07/02/2010 05:46 PM, Chris Fields wrote: > On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > > >> Hi guys! >> >> I'd like to thank you for this important project. I currently develop >> a script that uses the SeqIO module to read fasta or files with other >> bio-formats. However your installation instructions are too difficult >> to be followed, or even outdated, especially for the mac platform. >> >> After trying a week I really can't install bioperl on a Snow Leopard >> machine (perl 5.10.0) and I tried the CPAN and the fink method. None >> of them works! Especially cpan seems to mess up with itself and now >> doesn't install anything! >> > That's odd. Can you send me what you are seeing? > > >> As for the ubuntu platform a simple command like: "sudo apt-get >> install bioperl" simply does the trick! >> However I couldn't find this simple command in your installation >> guidelines, and I don't really understand why I should set up a >> server, before installing bioperl and then follow this complicated >> series of instructions, to achieve something that is so simple! >> > That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). > this depends on the age of your distribution rather than on what is apt-get-able from various places. Debian Squeeze has 1.6.1, and so does Ubuntu since Lucid. http://packages.qa.debian.org/b/bioperl.html https://launchpad.net/ubuntu/+source/bioperl > I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > > I am CCing the Debian-Med list just in case they have some better idea here, but what I suggest if you don't want to >> I understand that you try to give complete instructions for people who >> may be pleased with more advanced stuff, but please don't forget >> biology students who don't have a deep computational background. These >> guys like me would appreciate some simple stuff to get their job and >> their projects done, without needing to waste days to figure out >> complicated-guru stuff. >> > We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > The intention of us Debian- and Ubuntu-Helpers is very much also to help you X-core guys to concentrate on whatever you want to concentrate on and by taking as many of the "cannot build this or that" questions away from you as we possibly can. From our point of view, karmic or lenny are already rather ancient. As a BioPerl developer you probably don't want to run any of the packages in your routine anyway, so there is not much of a point to update for you. But I share your concern for production sites that want to sync with your vibrant development. If one wants to stay with binaries I see apt-pinning and backports.org. If one would just add the Debian sources of unstable to the /etc/apt/sources.list, then one could also very easily create distribution-adjusted packages oneself by apt-get source -b bioperl, which would then execute "the make" for you. The original request for a pointer to the Debian/Ubuntu packages would be nice, indeed. We'll see us at BOSC next week. If there is anything you think we should do to help your experience with the distributions then please drop us a line or grep for me in Boston. The segmentation is no problem for the packaging, but possibly more so for the regular user with a biological background. Best, Steffen From kai.blin at biotech.uni-tuebingen.de Sat Jul 3 03:05:26 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Sat, 03 Jul 2010 09:05:26 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <1278140726.2833.77.camel@gonzo.home.kblin.org> On Fri, 2010-07-02 at 10:46 -0500, Chris Fields wrote: Hi Chris, > > As for the ubuntu platform a simple command like: "sudo apt-get > > install bioperl" simply does the trick! > > However I couldn't find this simple command in your installation > > guidelines, and I don't really understand why I should set up a > > server, before installing bioperl and then follow this complicated > > series of instructions, to achieve something that is so simple! > > That's b/c the bioperl that is installed with apt is not up to date. > CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for > bioperl-run (where CPAN is at v.1.6.1). As Steffen already said, the current Ubuntu version is 1.6.1, for both bioperl and bioperl-run. I don't think providing backports for Debian/Ubuntu versions wouldn't be too hard. > I would like to get the releases to a point where they are easily > packaged for apt/yum/ppm/fink/macports/whatever, so any help along > those lines is greatly appreciated. There currently is only an "automated port" of Bioperl on the openSuse Build Service (OBS). I'll probably end up looking into packaging BioPerl for SLES11, and would do that on OBS. Supporting other suse distros is trivial, other RPM-based distros are doable once you figure out the package names. I'd say if Debian, Fedora, Suse and Ubuntu are covered, you're doing pretty fine for Linux. People using more exotic distros will be used to build their own stuff anyway. :) I've got no idea about packaging for OSX. > > I understand that you try to give complete instructions for people who > > may be pleased with more advanced stuff, but please don't forget > > biology students who don't have a deep computational background. These > > guys like me would appreciate some simple stuff to get their job and > > their projects done, without needing to waste days to figure out > > complicated-guru stuff. I think some of the instructions on installing BioPerl are pretty concise and allow you to just copy&paste the commands (see the ubuntu-server install instructions). They might be a bit outdated, I didn't check that. And of course I agree that it would be nicer if you could just point your package manager at the appropriate repository and be done. However, there's only a few people working on BioPerl, and packaging can eat a lot of time, as does keeping install instructions up-to-date. Especially on install instructions, every user can help. Once you wasted days on figuring out the complicated guru-stuff, write a wiki page to explain it in a less complicated way. :) Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From maizemu at gmail.com Sat Jul 3 11:30:14 2010 From: maizemu at gmail.com (Christopher Bottoms) Date: Sat, 3 Jul 2010 10:30:14 -0500 Subject: [Bioperl-l] Fwd: Codefest 2010: Final details In-Reply-To: References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> Message-ID: I will be there first thing Wednesday morning. I'd be glad to help work on any project. On Sat, Jul 3, 2010 at 9:15 AM, Chris Fields wrote: > I will be there on the afternoon of the 7th. There are a couple of > projects one can look into for Moose and Perl 6 (Biome and BioPerl6). I > think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not > sure where that is (might be surplanted by SQLite work?). Would be nice to > talk with Mark re: the wrapper system for BioPerl as well. > > So lots of stuff to think over and plan for. Maybe we should move this to > open-bio-l, or bioperl-l? > > chris (fields) > > On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote: > > > Chris, > > > > I do not have too much experience on cloud computing, either. There > > will be quite a few people from BioPerl . We'll meet and come up with > > a plan first thing in the morning. Unless someone has a very good one > > ready for sharing... > > > > -Heikki > > > > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho > > cell: +966 545 595 849 office: +966 2 808 2429 > > > > Computational Bioscience Research Centre (CBRC), Building #2, Office > #4216 > > 4700 King Abdullah University of Science and Technology (KAUST) > > Thuwal 23955-6900, Kingdom of Saudi Arabia > > > > > > > > > > On 3 July 2010 08:36, Christopher Bottoms wrote: > >> Hi all, > >> > >> I was originally planning on working on cloud computing at the Codefest. > >> However, the 2-day cloud computing tutorial that I was going to attend > in > >> mid June was canceled. Does anyone have any programming that they would > like > >> help with? I have experience with Perl 5, including Moose, and I am > starting > >> to dabble in Perl 6. I have also programmed in Java in the past. I hear > >> Python is easy to learn, so I'd be open to working on a Python project > as > >> well. > >> > >> Thanks, > >> Christopher Bottoms > >> > >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman > wrote: > >>> > >>> Hi all; > >>> Codefest 2010 is finally here: next Wednesday and Thursday at > >>> Harvard Medical School and Massachusetts General Hospital in > >>> beautiful Boston. All of the logistics, directions and details > >>> are on the wiki page: > >>> > >>> http://www.open-bio.org/wiki/Codefest_2010 > >>> > >>> If you want the short version: show up at Harvard Medical School on > >>> Wednesday at 10am and we'll take care of the rest. Thanks to the > >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll > >>> have coffee, lunches and internet. Thanks to Steffen and Ntino, > >>> we'll have Amazon credits to utilize. And of course, there will be > >>> BBQ and drinking on Thursday night when we are finished. > >>> > >>> I'm looking forward to a fun and productive time. The general plan > >>> will be to spend a bit of time on Wednesday morning organizing > >>> ourselves into like minded groups of folks, and then commence with > >>> coding and collaborating. > >>> > >>> If you aren't able to make it and you're listed on the wiki page under > >>> participants, please do cross your name off so we have a good idea of > >>> final numbers. Likewise, if you are coming but haven't put your name up > >>> there please add it. > >>> > >>> If you are interested in helping with making software and data > >>> available on shared cloud resources, here are the latest Amazon > >>> AMIs, snapshots, and the code base: > >>> > >>> Cloud BioLinux images: > >>> 64bit: ami-d62cc4bf > >>> 32bit: ami-5423cb3d > >>> > >>> An EBS public snapshot with indexed genomes: > >>> snap-67446d0f > >>> > >>> Infrastructure: > >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/ > >>> > >>> Send an e-mail with any questions, thoughts or concerns. My phone > >>> number is 617-447-8586 in case you end up hopelessly lost somewhere > >>> in Boston and are desperate to begin programming. > >>> > >>> Looking forward to seeing everyone next Wednesday, > >>> Brad > >> > >> > > From cjfields at illinois.edu Sat Jul 3 14:23:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:23:08 -0500 Subject: [Bioperl-l] Error when Using BLAT???? In-Reply-To: References: Message-ID: <1D738754-1FA5-40CB-B805-27A3A36FF319@illinois.edu> On Jun 29, 2010, at 8:58 AM, Minh Bui wrote: > Hi everyone, > I am writing an application that allows me to search through a database > (yeast.nt*) *with a few queries (yeastquery.fasta). Here is the code: > > *use warnings;* > *use Bio::Tools::Run::Alignment::Blat;* > *use Bio::SeqIO;* > *use Bio::DB::Fasta;* > * * > *my $seqio_object = Bio::SeqIO -> new (-file => > 'C:/Users/MINH/Desktop/yeastquery.fasta', -format => 'fasta'); * > * * > *my $database = 'C:/Users/MINH/Desktop/yeast.nt';* > *my $db = Bio::DB::Fasta->new($database); * > * * > *my $factory = Bio::Tools::Run::Alignment::Blat->new(); * > * > * > *while (my $blat_object = $seqio_object -> next_seq) {** * > * my $results = $factory -> run($blat_object,$db); * > *}* > > > BUT i got this error and don't know how to fix it. I am sorry, i am new to > Perl and Bioperl. I am using window 7, Strawberry. > > > *Replacement list is longer than search list at > C:/strawberry/perl/site/lib/Bio/Range.pm line 251.* > *Use of uninitialized value in concatenation (.) or string at > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm line 251, > line 1.* The above are warnings from perl 5.12 that can be ignored (they have been fixed in bioperl-live on github). > *'-out' is not recognized as an internal or external command,* > *operable program or batch file.* > * > * > *------------- EXCEPTION: Bio::Root::Exception -------------* > *MSG: Blat call ( -out=psl C:\Users\MINH\AppData\Local\Temp\BUiXTGzYC2 > C:\Users\MINH\AppData\Local\Temp\yQK5pzgJ_z) crashed: 256 * > * > * > *STACK: Error::throw* > *STACK: Bio::Root::Root::throw > C:/strawberry/perl/site/lib/Bio/Root/Root.pm:368* > *STACK: Bio::Tools::Run::Alignment::Blat::_run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:261* > *STACK: Bio::Tools::Run::Alignment::Blat::run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:178* > *STACK: D:/eclipswp/bioperl/readfasta.pl:15* > *-----------------------------------------------------------* > > Thank you for your help. That may be a bug; I can check on it (I'm planning on setting up a BLAT pipeline here in the next few days). chris From cjfields at illinois.edu Sat Jul 3 14:27:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:27:32 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: No comments. I'm assuming this is okay to merge into master branch, so will merge in later today. chris On Jun 30, 2010, at 12:35 PM, Chris Fields wrote: > All, > > I have a branch in github (topic/species_proxy) that converts > Bio::Species into a proxy class. This appears to fix a ton of problems > introduced during the Tree/Taxonomy refactoring a few years back. > > Advantages: > > 1) No need for Scalar::Util::weaken within Bio::Species or > Bio::Tree::Node. Cleanup methods are handled during instance > destruction. > > 2) This paves the way a bit more for eventual deprecation of > Bio::Species in 1.7. > > 3) Works with bioperl-db and BioSQL as is (passes on both my local > Ubuntu 9.10 and Mac OS X 10.6), perl 5.10 and 5.12, should work with > earlier perl versions. > > Disadvantages: > > 1) For every Bio::Species, we have a Bio::Taxon, a Bio::Tree::Tree, and > a Bio::DB::Taxonomy (one instance more than the previous Bio::Species > implementation). We can probably reduce that down considerably by > creating the needed instances lazily. > > This fixes: > > bug 3017 use threads to get genbank file error > bug 2594 Bio::Species memory leak > > and possibly others: > > bug 2773 Bio::Tree::Node gets destroyed even though it is still live > > If there are no comments, I'll merge this with the master branch in the > next few days. > > ++++++++++++++++++++++++++++++++++++++++++ > > (NOTE: skip the next two paragraphs if you don't want to read nasty > implementation details) > > Bio::Species had previously inherited from Bio::Taxon, but also required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). > > The above proxy fix converts Bio::Species into a proxy class, which only > inherits the interface (Bio::Tree::NodeI), and delegates to an internal > Bio::Taxon and a Bio::Tree::Tree. Neither contained object has a > reference back to the Bio::Species instance, thus the class can perform > proper garbage collection. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at drycafe.net Sat Jul 3 16:55:30 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 3 Jul 2010 16:55:30 -0400 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > Bio::Species had previously inherited from Bio::Taxon, but also > required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sat Jul 3 19:36:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 18:36:15 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> Message-ID: <57B6FE86-FF5E-4579-B3FB-A2D7AB366117@illinois.edu> On Jul 3, 2010, at 3:55 PM, Hilmar Lapp wrote: > On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > >> Bio::Species had previously inherited from Bio::Taxon, but also required >> it to hold a Bio::Tree::Tree which contained a circular reference back >> to the Bio::Species object, thus requiring Scalar::Util::weaken. This >> has caused several hard-to-diagnose problems with premature garbage >> collection, including some issues with threads (bug 3017). > > > Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? > > -hilmar In my experience, using weaken() is a bit of a 'code smell', and in general there are nice, sane ways to work around it. The solutions I outlined for the SeqI<->SeqFeatureI suggestion I thought made sense, if you think of Bio::SeqI as really more like a Bio::SeqRecord (has-a PrimarySeqI, does hold features, annotations, etc). There are no circular refs in this case: SeqI has-a SeqFeature(s)I, via FeatureHolderI SeqI has-a PrimarySeqI SeqFeatureI has-a PrimarySeqI Nothing refers back to SeqI It's a nice design decision and a great delegation of duties: SeqFeatures shouldn't need the Seq(Record) as a whole but the just the sequence itself, present as the PrimarySeqI, therefore they are attached to that. Any sequence-specific changes (methods, attributes) should therefore be in PrimarySeqI, and if needed could be delegated to for convenience from a relevant SeqI. In this particular instance (Bio::Species), there appeared to be a need to store a ref to the Tree (containing self) in self to implement the prior Bio::Species methods, thus requiring the use of weaken(). To me this was an indication that we really needed to rethink the design of the class. Maybe the containing instance (eg: Bio::Seq in this case) needs to hold the classification (as a Tree) and cache the relevant species NodeI (a Bio::Taxon). As we're still at the stage where we are using a Bio::Species, I pushed that functionality for the time being into the Bio::Species class: it has-a Bio::NodeI and a Bio::Tree::Tree, but neither refers back to the Bio::Species. We're planning on deprecating Bio::Species in future releases anyway, and reimplementing so that Bio::Seq is storing the Tree and the Bio::Taxon species node should be easy when the time comes. Actually, this probably suggests abstracting the simplest parts of that out into a common interface, which could be switched over to Bio::Seq when needed. May work on that a bit... chris From holland at eaglegenomics.com Mon Jul 5 06:06:56 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 5 Jul 2010 11:06:56 +0100 Subject: [Bioperl-l] Job opening at Eagle Message-ID: Hi all - thought this might be of interest to you. ==== Eagle Genomics is 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. With a number of exciting new projects on the horizon we're continuing to build up our team of talented and committed experts to help us deliver them. We are currently looking for a top-class developer to work on a wide range of complex projects. The role involves a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had at least 3 years prior experience developing code for bioinformatics projects. For this Perl/Ensembl role you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. Extensive experience programming in another language, particularly Java, is a bonus but not essential. In addition to your superb technical and customer service skills, you will also: * be able to communicate clearly and proactively, * 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, * be a self-starter and good at managing your own workload and responsibilities. You will also have had hands-on experience in at least two of the following: * SQL query design, * Open-source bioinformatics toolkits such as BioPerl, BioMart, BioSQL, etc., * Amazon EC2, * VMware, * Workflow/pipeline design (preferably using eHive or Taverna), * System and user documentation, * Developing and presenting training courses for users and developers. The successful candidate would be expected to work from our offices near Cambridge. 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. We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. The closing date is 23rd July. ==== cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From davila.marcela at gmail.com Mon Jul 5 08:57:01 2010 From: davila.marcela at gmail.com (Marcela Davila) Date: Mon, 5 Jul 2010 05:57:01 -0700 (PDT) Subject: [Bioperl-l] Infernal parser Message-ID: Hi there! I was wondering where I can set a different program directory (a local directory that has a different version of the Infernal package) rather than that specified in the ENV variable to run cmsearch while using Bio::Tools::Run::Infernal. Thanks! From cjfields at illinois.edu Mon Jul 5 11:19:13 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 10:19:13 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. chris On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > Hi there! > > I was wondering where I can set a different program directory (a local > directory that has a different version of the Infernal package) rather > than that specified in the ENV variable to run cmsearch while using > Bio::Tools::Run::Infernal. > > Thanks! > _______________________________________________ > 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 Jul 5 12:18:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 11:18:30 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: <0A2DAC96-808B-4583-B9F7-DBE44F9F9F86@illinois.edu> Marcela, After taking a look again and running a few local checks, I found that setting INFERNALDIR does work after all. I committed some code so that you can also explicitly set program_dir() as well, so the order of preference is: setting program_dir() > INFERNALDIR > PATH failing if an executable isn't found in any of those. That shouldn't be necessary, though (setting INFERNALDIR in your local env should suffice). Note that the Infernal wrapper only really supports Infernal 1.0 and up now, but the older releases still support pre-1.0 if you need them. chris On Jul 5, 2010, at 10:19 AM, Chris Fields wrote: > Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. > > chris > > On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > >> Hi there! >> >> I was wondering where I can set a different program directory (a local >> directory that has a different version of the Infernal package) rather >> than that specified in the ENV variable to run cmsearch while using >> Bio::Tools::Run::Infernal. >> >> Thanks! >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Tue Jul 6 08:37:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 6 Jul 2010 13:37:05 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl Message-ID: Hello, I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the set of scripts in BioPerl. Below is what I have so far. The script works by reading in a GFF of 'repeat_region's and a fasta file of sequences. It outputs a fasta sequence file with the repeats replaced by Xs. The script clearly needs to be more configurable, but I thought I'd send it along now to see if I'm working along the right lines, or if I should be using a different approach. Comments? Cheers, Dan. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $seq_file; my $gff_file; GetOptions ( "verbose" => \$verbose, "seq=s" => \$seq_file, "gff=s" => \$gff_file, ) or die "failed to parse command line options\n"; die "fail $gff_file : $!\n" unless -s $gff_file; ## Set up the BioPerl objects my $seq_reader = Bio::SeqIO->new( -file => $seq_file, -format => 'fasta' ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => 'fasta', -width => 80 ); my $gff_reader = Bio::FeatureIO->new( -file => $gff_file, -format => 'GFF', ); #warn $seq_reader->width, "\n"; exit; ## Run my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>1){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq 'repeat_region'){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } # Debugging #last if $c > 100; } warn "read $c repeat_region features for ", scalar keys(%repeats), " sequences\n"; ## while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; print length($sequence), "\n" if $verbose > 0; for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, 'X' x ($end - $start)); } print length($sequence), "\n" if $verbose > 0; $seq->seq($sequence); $seq_writer->write_seq($seq); # Debugging; #last; } warn "OK\n"; From armendarez77 at hotmail.com Tue Jul 6 10:23:55 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 07:23:55 -0700 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From sharmashalu.bio at gmail.com Tue Jul 6 10:48:58 2010 From: sharmashalu.bio at gmail.com (shalu sharma) Date: Tue, 6 Jul 2010 10:48:58 -0400 Subject: [Bioperl-l] Intergenomic sequences Message-ID: Hi All, This is not a bioperl question but i thought someone might know the answer. Is there any package/program to find intergenic sequences? I would really appreciate your help. Thanks Shalu From bosborne11 at verizon.net Tue Jul 6 10:36:18 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:36:18 +0200 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: > > Hello, > > I'm designing degenerate primers using > Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 > Ns, but on some sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 6 10:50:25 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:50:25 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: =head1 NAME bioflat_index.pl - index sequence files using Bio::DB::Flat =head1 DESCRIPTION Create or update a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed. =head1 USAGE bioflat_index.pl file1 file2 file3... Options: --create Create or reinitialize the index. If not specified, the index must already exist. --format The format of the sequence files. Must be one of "genbank", "swissprot", "embl" or "fasta". --location Path to the directory in which the index files are stored. --dbname The symbolic name of the database to be created. --indextype Type of index to create. Either "bdb" or "flat". "binarysearch" is the same as "flat". Options can be abbreviated. For example, use -i for --indextype. The following environment variables will be used as defaults if the corresponding options are not provided: OBDA_FORMAT format of sequence file OBDA_LOCATION path to directory in which index files are stored OBDA_DBNAME name of database OBDA_INDEX type of index to create =cut On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > Hello, > > I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the > set of scripts in BioPerl. Below is what I have so far. The script > works by reading in a GFF of 'repeat_region's and a fasta file of > sequences. It outputs a fasta sequence file with the repeats replaced > by Xs. > > The script clearly needs to be more configurable, but I thought I'd > send it along now to see if I'm working along the right lines, or if I > should be using a different approach. > > Comments? > > > Cheers, > Dan. > > > > #!/usr/bin/perl -w > > use strict; > use Getopt::Long; > > use Bio::SeqIO; > use Bio::FeatureIO; > > > > ## Set options > > my $verbose = 0; > my $seq_file; > my $gff_file; > > GetOptions > ( > "verbose" => \$verbose, > "seq=s" => \$seq_file, > "gff=s" => \$gff_file, > ) > or die "failed to parse command line options\n"; > > die "fail $gff_file : $!\n" > unless -s $gff_file; > > > > ## Set up the BioPerl objects > > my $seq_reader = > Bio::SeqIO->new( -file => $seq_file, > -format => 'fasta' > ); > > my $seq_writer = > Bio::SeqIO->new( -fh => \*STDOUT, > -format => 'fasta', > -width => 80 > ); > > my $gff_reader = > Bio::FeatureIO->new( -file => $gff_file, > -format => 'GFF', > ); > > #warn $seq_reader->width, "\n"; exit; > > > > ## Run > > my (%repeats, $c); > > while ( my $feature = $gff_reader->next_feature() ) { > if($verbose>1){ > print > join("\t", #$feature, > $feature->seq_id, > $feature->type->name, > $feature->start, > $feature->end, > ), "\n"; > } > > if($feature->type->name eq 'repeat_region'){ > $c++; > push @{$repeats{ $feature->seq_id }}, > [$feature->start, > $feature->end]; > } > > # Debugging > #last if $c > 100; > } > > warn "read $c repeat_region features for ", > scalar keys(%repeats), " sequences\n"; > > > > ## > > while(my $seq = $seq_reader->next_seq){ > my $id = $seq->id; > my $sequence = $seq->seq; > > print $id, "\n" > if $verbose > 0; > > print length($sequence), "\n" > if $verbose > 0; > > for my $region (@{$repeats{ $id }}){ > my ($start, $end) = @$region; > print "$start\t$end\n" > if $verbose > 1; > > substr($sequence, $start, $end - $start, 'X' x ($end - $start)); > } > > print length($sequence), "\n" > if $verbose > 0; > > $seq->seq($sequence); > > $seq_writer->write_seq($seq); > > # Debugging; > #last; > } > > warn "OK\n"; > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From armendarez77 at hotmail.com Tue Jul 6 11:58:11 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 08:58:11 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: Hi Brian, This sort of worked. The script still dies with the same complaint when the primer sequence is 19 bases long and starts with an 'n': Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't look very DNA to me at .... However, other 19bp long sequences with 3 internal n's are allowed. Is there another way to prevent the script from dying when it comes across these sequences or should I just not allow these sequences to be processed? Thanks, Veronica Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From roy.chaudhuri at gmail.com Tue Jul 6 12:31:04 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 06 Jul 2010 17:31:04 +0100 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: <4C335A48.8000006@gmail.com> Hi Veronica, Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. Cheers. Roy. On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > > Hi Brian, > > This sort of worked. The script still dies with the same complaint > when the primer sequence is 19 bases long and starts with an 'n': > > Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > look very DNA to me at .... > > > However, other 19bp long sequences with 3 internal n's are allowed. > Is there another way to prevent the script from dying when it comes > across these sequences or should I just not allow these sequences to > be processed? > > Thanks, > > Veronica > > Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > > > > Veronica, Yes, when you're making your sequence object do something > like: -alphabet => 'dna' For example: use Bio::Seq; > > $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > PM, wrote: > Hello, > > I'm designing degenerate primers using Bio::Tools::Primer3 and > Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to > catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > Bioperl-l mailing list Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > 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 Jul 6 13:17:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 12:17:03 -0500 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <4C335A48.8000006@gmail.com> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> <4C335A48.8000006@gmail.com> Message-ID: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! chris On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > Hi Veronica, > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > Cheers. > Roy. > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: >> >> Hi Brian, >> >> This sort of worked. The script still dies with the same complaint >> when the primer sequence is 19 bases long and starts with an 'n': >> >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't >> look very DNA to me at .... >> >> >> However, other 19bp long sequences with 3 internal n's are allowed. >> Is there another way to prevent the script from dying when it comes >> across these sequences or should I just not allow these sequences to >> be processed? >> >> Thanks, >> >> Veronica >> >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com >> >> >> >> Veronica, Yes, when you're making your sequence object do something >> like: -alphabet => 'dna' For example: use Bio::Seq; >> >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 >> PM, wrote: >> Hello, >> >> I'm designing degenerate primers using Bio::Tools::Primer3 and >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some >> sequences the script dies with the following error: >> >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't >> look very DNA to me at Perl.pm line 629. >> >> >> >> I couldn't find any information on this error. Is there a way to >> catch or override it? >> >> Thank you, >> >> Veronica >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 6 14:21:10 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 11:21:10 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> References: , ,,<1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , , , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net>, , <4C335A48.8000006@gmail.com>, <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Message-ID: Thank you. The missing 'n' was the problem. Veronica > From: cjfields at illinois.edu > Date: Tue, 6 Jul 2010 12:17:03 -0500 > To: roy.chaudhuri at gmail.com > CC: bioperl-l at lists.open-bio.org; bosborne11 at verizon.net; armendarez77 at hotmail.com > Subject: Re: [Bioperl-l] 85% ATGCN > > Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! > > chris > > On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > > > Hi Veronica, > > > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > > > Cheers. > > Roy. > > > > > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > >> > >> Hi Brian, > >> > >> This sort of worked. The script still dies with the same complaint > >> when the primer sequence is 19 bases long and starts with an 'n': > >> > >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > >> look very DNA to me at .... > >> > >> > >> However, other 19bp long sequences with 3 internal n's are allowed. > >> Is there another way to prevent the script from dying when it comes > >> across these sequences or should I just not allow these sequences to > >> be processed? > >> > >> Thanks, > >> > >> Veronica > >> > >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > >> > >> > >> > >> Veronica, Yes, when you're making your sequence object do something > >> like: -alphabet => 'dna' For example: use Bio::Seq; > >> > >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > >> PM, wrote: > >> Hello, > >> > >> I'm designing degenerate primers using Bio::Tools::Primer3 and > >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > >> sequences the script dies with the following error: > >> > >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > >> look very DNA to me at Perl.pm line 629. > >> > >> > >> > >> I couldn't find any information on this error. Is there a way to > >> catch or override it? > >> > >> Thank you, > >> > >> Veronica > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >> > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From kellert at ohsu.edu Tue Jul 6 17:54:36 2010 From: kellert at ohsu.edu (Tom Keller) Date: Tue, 6 Jul 2010 14:54:36 -0700 Subject: [Bioperl-l] SeqIO tag/location question Message-ID: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Greetings, A genbank file I am working with has features: exon 37167..37302 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=24 exon 39189..39256 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=25 exon 48058..50644 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=26 When I parse it using: my $db = Bio::DB::RefSeq->new(); my $seq = $db->get_Seq_by_acc($accession); my @features = $seq->get_SeqFeatures; for my$feat_obj ( @features ) { if ($feat_obj->primary_tag eq 'exon') { print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; for my $tag ($feat_obj->get_all_tags) { for my $value ($feat_obj->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } } I get the following: primary tag: exon start: 42167 end: 42302 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 24 primary tag: exon start: 44189 end: 44256 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 25 primary tag: exon start: 53058 end: 55644 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 26 Where does the discrepancy in location (+5000) come from? thanks for your help, Tom MMI DNA Services Core Facility 4-2442 kellert at ohsu.edu RJH (CROET/BasicScience) 6339b From cjfields at illinois.edu Tue Jul 6 19:10:18 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 18:10:18 -0500 Subject: [Bioperl-l] SeqIO tag/location question In-Reply-To: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> References: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Message-ID: <0DBD5366-A92B-4A70-B882-7E8FA88A85B0@illinois.edu> RefSeq pulls the file from EBI, not from NCBI (IIRC), so maybe there is a difference between the two versions? Hard to say w/o knowing the exact accession. chris On Jul 6, 2010, at 4:54 PM, Tom Keller wrote: > Greetings, > A genbank file I am working with has features: > exon 37167..37302 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=24 > exon 39189..39256 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=25 > exon 48058..50644 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=26 > > When I parse it using: > my $db = Bio::DB::RefSeq->new(); > my $seq = $db->get_Seq_by_acc($accession); > my @features = $seq->get_SeqFeatures; > for my$feat_obj ( @features ) { > if ($feat_obj->primary_tag eq 'exon') { > print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; > for my $tag ($feat_obj->get_all_tags) { > for my $value ($feat_obj->get_tag_values($tag)) { > print " value: ", $value, "\n"; > } > } > } > } > > I get the following: > primary tag: exon start: 42167 end: 42302 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 24 > primary tag: exon start: 44189 end: 44256 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 25 > primary tag: exon start: 53058 end: 55644 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 26 > > Where does the discrepancy in location (+5000) come from? > > thanks for your help, > Tom > MMI DNA Services Core Facility > 4-2442 > kellert at ohsu.edu > RJH (CROET/BasicScience) 6339b > > > > > > > _______________________________________________ > 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 Tue Jul 6 19:14:15 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 7 Jul 2010 00:14:15 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Cheers Brian! Do you think this script will work if I allow sequence and feature '-format's to be picked by the user among all those listed as valid file formats in BioPerl? http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS Or should I stick to Fasta/GFF (or some other implementation)? Cheers, Dan. On 6 July 2010 15:50, Brian Osborne wrote: > Dan, > > There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: > > =head1 NAME > > bioflat_index.pl - index sequence files using Bio::DB::Flat > > =head1 DESCRIPTION > > ?Create or update a biological sequence database indexed with the > ?Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files > ?containing the sequence information to be indexed. > > =head1 USAGE > > ?bioflat_index.pl file1 file2 file3... > > ?Options: > > ? ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, > ? ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. > > ? ? --format ? ? The format of the sequence files. ?Must be one > ? ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". > > ? ? --location ? ? Path to the directory in which the index files > ? ? ? ? ? ? ? ? ? ? ? ? ? are stored. > > ? ? --dbname ? ? ? The symbolic name of the database to be created. > > ? ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". > ? ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". > > Options can be abbreviated. ?For example, use -i for --indextype. > > The following environment variables will be used as defaults if the > corresponding options are not provided: > > ? ? OBDA_FORMAT ? ? ?format of sequence file > ? ? OBDA_LOCATION ? ?path to directory in which index files are stored > ? ? OBDA_DBNAME ? ? ?name of database > ? ? OBDA_INDEX ? ? ? type of index to create > > =cut > > > On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > >> Hello, >> >> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >> set of scripts in BioPerl. Below is what I have so far. The script >> works by reading in a GFF of 'repeat_region's and a fasta file of >> sequences. It outputs a fasta sequence file with the repeats replaced >> by Xs. >> >> The script clearly needs to be more configurable, but I thought I'd >> send it along now to see if I'm working along the right lines, or if I >> should be using a different approach. >> >> Comments? >> >> >> Cheers, >> Dan. >> >> >> >> #!/usr/bin/perl -w >> >> use strict; >> use Getopt::Long; >> >> use Bio::SeqIO; >> use Bio::FeatureIO; >> >> >> >> ## Set options >> >> my $verbose = 0; >> my $seq_file; >> my $gff_file; >> >> GetOptions >> ?( >> ? "verbose" => \$verbose, >> ? "seq=s" => \$seq_file, >> ? "gff=s" => \$gff_file, >> ?) >> ?or die "failed to parse command line options\n"; >> >> die "fail $gff_file : $!\n" >> ?unless -s $gff_file; >> >> >> >> ## Set up the BioPerl objects >> >> my $seq_reader = >> ?Bio::SeqIO->new( -file => $seq_file, >> ? ? ? ? ? ? ? ? ?-format => 'fasta' >> ? ? ? ? ? ? ? ?); >> >> my $seq_writer = >> ?Bio::SeqIO->new( -fh => \*STDOUT, >> ? ? ? ? ? ? ? ? ?-format => 'fasta', >> ? ? ? ? ? ? ? ? ?-width => 80 >> ? ? ? ? ? ? ? ?); >> >> my $gff_reader = >> ?Bio::FeatureIO->new( -file => $gff_file, >> ? ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >> ? ? ? ? ? ? ? ? ? ?); >> >> #warn $seq_reader->width, "\n"; exit; >> >> >> >> ## Run >> >> my (%repeats, $c); >> >> while ( my $feature = $gff_reader->next_feature() ) { >> ?if($verbose>1){ >> ? ?print >> ? ? ?join("\t", #$feature, >> ? ? ? ? ?$feature->seq_id, >> ? ? ? ? ?$feature->type->name, >> ? ? ? ? ?$feature->start, >> ? ? ? ? ?$feature->end, >> ? ? ? ? ), "\n"; >> ?} >> >> ?if($feature->type->name eq 'repeat_region'){ >> ? ?$c++; >> ? ?push @{$repeats{ $feature->seq_id }}, >> ? ? ?[$feature->start, >> ? ? ? $feature->end]; >> ?} >> >> ?# Debugging >> ?#last if $c > 100; >> } >> >> warn "read $c repeat_region features for ", >> ?scalar keys(%repeats), " sequences\n"; >> >> >> >> ## >> >> while(my $seq = $seq_reader->next_seq){ >> ?my $id = $seq->id; >> ?my $sequence = $seq->seq; >> >> ?print $id, "\n" >> ? ?if $verbose > 0; >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?for my $region (@{$repeats{ $id }}){ >> ? ?my ($start, $end) = @$region; >> ? ?print "$start\t$end\n" >> ? ? ?if $verbose > 1; >> >> ? ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >> ?} >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?$seq->seq($sequence); >> >> ?$seq_writer->write_seq($seq); >> >> ?# Debugging; >> ?#last; >> } >> >> warn "OK\n"; >> _______________________________________________ >> 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 Jul 7 05:42:59 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 07 Jul 2010 11:42:59 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, In my opinion the user should be able to use any supported format as input, yes. Brian O. On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > Cheers Brian! > > Do you think this script will work if I allow sequence and feature > '-format's to be picked by the user among all those listed as valid > file formats in BioPerl? > > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats > http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS > > > Or should I stick to Fasta/GFF (or some other implementation)? > > Cheers, > Dan. > > > On 6 July 2010 15:50, Brian Osborne wrote: >> Dan, >> >> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >> >> =head1 NAME >> >> bioflat_index.pl - index sequence files using Bio::DB::Flat >> >> =head1 DESCRIPTION >> >> Create or update a biological sequence database indexed with the >> Bio::DB::Flat indexing scheme. The arguments are a list of flat files >> containing the sequence information to be indexed. >> >> =head1 USAGE >> >> bioflat_index.pl file1 file2 file3... >> >> Options: >> >> --create Create or reinitialize the index. If not specified, >> the index must already exist. >> >> --format The format of the sequence files. Must be one >> of "genbank", "swissprot", "embl" or "fasta". >> >> --location Path to the directory in which the index files >> are stored. >> >> --dbname The symbolic name of the database to be created. >> >> --indextype Type of index to create. Either "bdb" or "flat". >> "binarysearch" is the same as "flat". >> >> Options can be abbreviated. For example, use -i for --indextype. >> >> The following environment variables will be used as defaults if the >> corresponding options are not provided: >> >> OBDA_FORMAT format of sequence file >> OBDA_LOCATION path to directory in which index files are stored >> OBDA_DBNAME name of database >> OBDA_INDEX type of index to create >> >> =cut >> >> >> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >> >>> Hello, >>> >>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>> set of scripts in BioPerl. Below is what I have so far. The script >>> works by reading in a GFF of 'repeat_region's and a fasta file of >>> sequences. It outputs a fasta sequence file with the repeats replaced >>> by Xs. >>> >>> The script clearly needs to be more configurable, but I thought I'd >>> send it along now to see if I'm working along the right lines, or if I >>> should be using a different approach. >>> >>> Comments? >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> #!/usr/bin/perl -w >>> >>> use strict; >>> use Getopt::Long; >>> >>> use Bio::SeqIO; >>> use Bio::FeatureIO; >>> >>> >>> >>> ## Set options >>> >>> my $verbose = 0; >>> my $seq_file; >>> my $gff_file; >>> >>> GetOptions >>> ( >>> "verbose" => \$verbose, >>> "seq=s" => \$seq_file, >>> "gff=s" => \$gff_file, >>> ) >>> or die "failed to parse command line options\n"; >>> >>> die "fail $gff_file : $!\n" >>> unless -s $gff_file; >>> >>> >>> >>> ## Set up the BioPerl objects >>> >>> my $seq_reader = >>> Bio::SeqIO->new( -file => $seq_file, >>> -format => 'fasta' >>> ); >>> >>> my $seq_writer = >>> Bio::SeqIO->new( -fh => \*STDOUT, >>> -format => 'fasta', >>> -width => 80 >>> ); >>> >>> my $gff_reader = >>> Bio::FeatureIO->new( -file => $gff_file, >>> -format => 'GFF', >>> ); >>> >>> #warn $seq_reader->width, "\n"; exit; >>> >>> >>> >>> ## Run >>> >>> my (%repeats, $c); >>> >>> while ( my $feature = $gff_reader->next_feature() ) { >>> if($verbose>1){ >>> print >>> join("\t", #$feature, >>> $feature->seq_id, >>> $feature->type->name, >>> $feature->start, >>> $feature->end, >>> ), "\n"; >>> } >>> >>> if($feature->type->name eq 'repeat_region'){ >>> $c++; >>> push @{$repeats{ $feature->seq_id }}, >>> [$feature->start, >>> $feature->end]; >>> } >>> >>> # Debugging >>> #last if $c > 100; >>> } >>> >>> warn "read $c repeat_region features for ", >>> scalar keys(%repeats), " sequences\n"; >>> >>> >>> >>> ## >>> >>> while(my $seq = $seq_reader->next_seq){ >>> my $id = $seq->id; >>> my $sequence = $seq->seq; >>> >>> print $id, "\n" >>> if $verbose > 0; >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> for my $region (@{$repeats{ $id }}){ >>> my ($start, $end) = @$region; >>> print "$start\t$end\n" >>> if $verbose > 1; >>> >>> substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>> } >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> $seq->seq($sequence); >>> >>> $seq_writer->write_seq($seq); >>> >>> # Debugging; >>> #last; >>> } >>> >>> warn "OK\n"; >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From gb7 at sanger.ac.uk Wed Jul 7 10:41:13 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Wed, 07 Jul 2010 15:41:13 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes Message-ID: <4C349209.6030209@sanger.ac.uk> Hi. I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? Thanks. Greg. -- 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 heikki.lehvaslaiho at gmail.com Wed Jul 7 13:14:21 2010 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 7 Jul 2010 20:14:21 +0300 Subject: [Bioperl-l] BLAT Howto? In-Reply-To: References: Message-ID: There are BLAT and SSAHA that have been around for some time. For next gen sequences, there are more algorithms coming up all the time. Have a look at e.g. Li and Homer in Briefings in Bioinformatics "A survey of sequence alignment algorithms for next-generation sequencing". -Heikki On 28 June 2010 16:15, Minh Bui wrote: > Hi everyone, > I am new to Bioperl and perl itself and running perl on window 7. > > ?My job is to develop an application that can search through a ?database > with thousands of queries. BLAT is a ?best option (if you know any other > algorithm that can do this, please let me know). I have been searching > through Bioperl BLAT documentation and there is only one document for BLAT > but without example. > I am wondering if anyone has done BLAT using Bioperl, please show me how to > use BLAT in ?Bioperl. > > Thank you very much and sorry for my english. Its not my first language. > _______________________________________________ > 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 Jul 7 22:36:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jul 2010 21:36:22 -0500 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: It is possible our NEXUS parser doesn't do this for some reason, but we would need a sample file to work out the problem. You could try Rutger Vos's Bio::Phylo, which may have this working. chris On Jul 7, 2010, at 9:41 AM, Greg Baillie wrote: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. > > In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. > > Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? > > Thanks. > > Greg. > > > > -- > 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. _______________________________________________ > 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 Jul 8 00:27:56 2010 From: jason at bioperl.org (Jason Stajich) Date: Wed, 07 Jul 2010 21:27:56 -0700 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: <4C3553CC.8030400@bioperl.org> Hi - Is this just that you have internal nodes labeled with the bootstrap/posterior value? If so you just want the node ids for the internal nodes then. The semantics of what is encoded in the internal nodes is not forced by the nexus format so it assumes they are ids by default. You can call $tree->move_id_to_bootstrap to migrate the ids of internal nodes to the bootstrap option. you can also use the -internal_node_id => 'bootstrap' option when initializing TreeIO objects too: =head2 new Title : new Usage : my $obj = Bio::TreeIO->new(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args : a hash. useful keys: -format : Specify the format of the file. Supported formats: newick Newick tree format nexus Nexus tree format nhx NHX tree format svggraph SVG graphical representation of tree tabtree ASCII text representation of tree lintree lintree output format -internal_node_id : what is stored in the internal node ids, bootstrap values or ids, coded as 'bootstrap' or 'id' -jason Greg Baillie wrote, On 7/7/10 7:41 AM: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of > trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I > iterate through the nodes looking for posterior values (/if ( > $node->has_tag('posterior') ) {.../), none of the nodes seem to have > posteriors. > > In fact, none of the nodes have any tags (/my @tags = > $node->get_all_tags(); print join ',', @tags/). And when I dump an > entire tree using Data::Dumper, there is no sign of any of the node > values. > > Does TreeIO handle these values? If so, should I be looking somewhere > other than the tags for the values? > > Thanks. > > Greg. From gb7 at sanger.ac.uk Thu Jul 8 10:24:14 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Thu, 08 Jul 2010 15:24:14 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C3553CC.8030400@bioperl.org> References: <4C349209.6030209@sanger.ac.uk> <4C3553CC.8030400@bioperl.org> Message-ID: <4C35DF8E.1050905@sanger.ac.uk> Hi Jason. I'm trying to get access to the posterior probability value, rate, etc, that are stored within open-square-bracket-ampersand and close-square-bracket ([&]) blocks in the tree string. It appears that this information is stripped out during the parsing of the tree string (I have tried to get it from the $node->bootstrap()). I'm having trouble identifying the module that parses the tree string - I thought I might be able to modify that. Any suggestions where I might find the appropriate code? In the meantime, I'll look at the Bio::Phylo modules (as per Chris' suggestion) to see if they have a way of handling that info. Thanks. Greg. Jason Stajich wrote: > Hi - > > Is this just that you have internal nodes labeled with the > bootstrap/posterior value? If so you just want the node ids for the > internal nodes then. The semantics of what is encoded in the internal > nodes is not forced by the nexus format so it assumes they are ids by > default. > You can call $tree->move_id_to_bootstrap > to migrate the ids of internal nodes to the bootstrap option. > > you can also use the -internal_node_id => 'bootstrap' option when > initializing TreeIO objects too: > > =head2 new > > Title : new > Usage : my $obj = Bio::TreeIO->new(); > Function: Builds a new Bio::TreeIO object > Returns : Bio::TreeIO > Args : a hash. useful keys: > -format : Specify the format of the file. Supported formats: > > newick Newick tree format > nexus Nexus tree format > nhx NHX tree format > svggraph SVG graphical representation of tree > tabtree ASCII text representation of tree > lintree lintree output format > -internal_node_id : what is stored in the internal node ids, > bootstrap values or ids, coded as > 'bootstrap' or 'id' > > -jason > Greg Baillie wrote, On 7/7/10 7:41 AM: >> Hi. >> >> I'm trying to extract information (eg. posterior values) from nodes >> of trees generated using BEAST/treeannotator/FigTree. >> >> The trees, which are in nexus format, seem to load OK, but when I >> iterate through the nodes looking for posterior values (/if ( >> $node->has_tag('posterior') ) {.../), none of the nodes seem to have >> posteriors. >> >> In fact, none of the nodes have any tags (/my @tags = >> $node->get_all_tags(); print join ',', @tags/). And when I dump an >> entire tree using Data::Dumper, there is no sign of any of the node >> values. >> >> Does TreeIO handle these values? If so, should I be looking somewhere >> other than the tags for the values? >> >> Thanks. >> >> Greg. -- 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 dan.bolser at gmail.com Thu Jul 8 10:33:19 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 15:33:19 +0100 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) Message-ID: The bugtracker seems broken (or taking a painfully long time to log me in). So here is my bug report before I forget: Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace Body: The code had inconsistent use of the '_qualify' function, and one instance of a hard-coded table name. These issues were not apparent until "-namespace anything" was used. First I got the fatal error: DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 428, line 2. which was due to a hard-coded table name. Then, after fixing, I got the error: Loading bulk data into database...DBD::mysql::db do failed: Table 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 570, line 10000. i.e. the prefix was being added to the table name twice. I went through the code and tried to make all references to table names consistent to ensure that bugs like this won't creep in again... however, the code for this module isn't very consistent. (See patch attached). -------------- next part -------------- A non-text attachment was scrubbed... Name: mysql.pm.patch Type: text/x-patch Size: 11908 bytes Desc: not available URL: From dan.bolser at gmail.com Thu Jul 8 12:06:59 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 17:06:59 +0100 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) Message-ID: Editing subject to see if it gets through... On 8 July 2010 15:33, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > From lincoln.stein at gmail.com Thu Jul 8 12:24:38 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:24:38 -0400 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) In-Reply-To: References: Message-ID: My code is never very consistent, unfortunately. Thanks for the patch, but it wasn't attached to the forwarded email. Could you try again? Lincoln On Thu, Jul 8, 2010 at 12:06 PM, Dan Bolser wrote: > Editing subject to see if it gets through... > > On 8 July 2010 15:33, Dan Bolser wrote: > > The bugtracker seems broken (or taking a painfully long time to log me > > in). So here is my bug report before I forget: > > > > > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > > > Body: > > The code had inconsistent use of the '_qualify' function, and one > > instance of a hard-coded table name. These issues were not apparent > > until "-namespace anything" was used. > > > > First I got the fatal error: > > > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 428, line 2. > > > > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > > > Loading bulk data into database...DBD::mysql::db do failed: Table > > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 570, line 10000. > > > > > > i.e. the prefix was being added to the table name twice. > > > > > > I went through the code and tried to make all references to table > > names consistent to ensure that bugs like this won't creep in again... > > however, the code for this module isn't very consistent. > > > > (See patch attached). > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform 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 Thu Jul 8 12:28:14 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:28:14 -0400 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) In-Reply-To: References: Message-ID: Never mind. I found the patch in the earlier message. Thanks again for tracking down the issues. Lincoln On Thu, Jul 8, 2010 at 10:33 AM, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From David.Messina at sbc.su.se Thu Jul 8 14:27:13 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jul 2010 14:27:13 -0400 Subject: [Bioperl-l] added -type for Bio::Annotation::DBLink Message-ID: Hi everybody, In working on representing sequence metadata*, I've found it useful to track the type of information that is involved in a database cross-reference. I'm adding an optional -type property to Bio::Annotation::DBLink to support this cleanly in BioPerl. Here follows my rationale. I'm not tied to doing this in B:A::DBLink if there's a better way ? it just seems the best route to me at the moment. -- So, what do I mean by tracking the type of information in a DB crossreference? Right now, a standard DBLink contains database => RefSeq ID => NM_12345 along with a few other optional properties. See the docs for details: http://doc.bioperl.org/bioperl-live/Bio/Annotation/DBLink.html I want to be able to say database => RefSeq ID => NM_12345 type => RNA Why? Two reasons: 1. a single database can store more than one type of information. RefSeq, for example, stores RNA and protein records. Although RefSeq's IDs are named intelligently to note their type (NM_xxx for transcript, NP_xxx for protein), this is not true for all databases and not everybody knows the ID codes. For example, here are three database-ID pairs: Genbank: AK291692.1 Genbank: CH471055.1 Genbank: AAH14616.1 Those are three different record types (mRNA, genomic DNA, protein) from the same database. 2. There can be multiple crossreferences for multiple types of information. There can be multiple source databases providing the same type of crossreference and multiple types of crossreferences. Take this example: Genbank: AAA81779.1 EMBL: AK291692 Ensembl: ENST00000308775 HPA: CAB001960 Two of these are mRNA records, one is a protein record, and one is something else entirely. If I wanted to take one mRNA xref and one protein xref from this set, I couldn't do it using solely the information provided above. If I had type information, though, it'd be easy. And since -type is an optional parameter, it is fully backwards-compatible. Any thoughts or comments? Dave * specifically, in SeqXML. See http://seqxml.org and http://doc.bioperl.org/bioperl-live/Bio/SeqIO/seqxml.html From abhishek.vit at gmail.com Fri Jul 9 11:02:09 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jul 2010 11:02:09 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO Message-ID: Hi (Chris) I feel I might be hitting a bug or missing something. I am trying to convert a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO for more clarity. I think the quality line is missing and the read is breaking into two lines. Any obvious mistakes ? Thanks! -Abhi ## Reading the FASTQ ASCII-64 file my $in = Bio::SeqIO->new( -format => 'fastq', -variant => 'illumina', -file => "<$in_fastq_file", ); ## File Handle for writing ASCII-33 (sanger) standard format my $out = Bio::SeqIO->new ( -format => 'fastq', -variant => 'sanger', -file => ">$out_fastq_file", ); while (my $oneread = $in->next_seq){ $out->write_seq($oneread); } Output: >HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCA AGGATATTGGTCTAA Input: @HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCAAGGATATTGGTCTAA +HWI-EAS397_0006:6:1:1023:19461#0/1 ^aYa^\a^aaaa\]a^^^^^]]]^L^Y]]]aa\`YZ^a]]a[a^^^^^`I^^^`]aaaa]]^]R`W^``^BBBBB From snoze.pa at gmail.com Fri Jul 9 15:06:31 2010 From: snoze.pa at gmail.com (snoze pa) Date: Fri, 9 Jul 2010 14:06:31 -0500 Subject: [Bioperl-l] MSG: Unrecognized DBSOURCE data: pdb: molecule Message-ID: Dear Users, While adding a genebank file to bioperl biosql database i am getting following error. Any Idea or help will be highly appreciated. Thank you s --------------------- WARNING --------------------- MSG: Unrecognized DBSOURCE data: pdb: molecule From biopython at maubp.freeserve.co.uk Sat Jul 10 07:43:47 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:43:47 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: > Hi (Chris) > > I feel I might be hitting a bug or missing something. I am trying to convert > a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO > for more clarity. I think the quality line is missing and the read is > breaking into two lines. > > Any obvious mistakes ? > > Thanks! > -Abhi It looks like you are getting FASTQ out rather than FASTQ (notice in addition to missing the qualities, the record starts with ">" rather than "@". Strange, as you do seem to be using the right FASTQ format and variant names. You could try using format="fastq-sanger" and format="fastq-illumina" rather than setting variant, to see if that changes anything. Peter From biopython at maubp.freeserve.co.uk Sat Jul 10 07:44:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:44:48 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: > On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >> Hi (Chris) >> >> I feel I might be hitting a bug or missing something. I am trying to convert >> a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO >> for more clarity. I think the quality line is missing and the read is >> breaking into two lines. >> >> Any obvious mistakes ? >> >> Thanks! >> -Abhi > > It looks like you are getting FASTQ out rather than FASTQ (notice in addition to > missing the qualities, the record starts with ">" rather than "@". Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) Peter From cjfields at illinois.edu Sat Jul 10 15:23:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jul 2010 14:23:30 -0500 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Jul 10, 2010, at 6:44 AM, Peter wrote: > On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >>> Hi (Chris) >>> >>> I feel I might be hitting a bug or missing something. I am trying to convert >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO >>> for more clarity. I think the quality line is missing and the read is >>> breaking into two lines. >>> >>> Any obvious mistakes ? >>> >>> Thanks! >>> -Abhi >> >> It looks like you are getting FASTQ out rather than FASTQ (notice in addition to >> missing the qualities, the record starts with ">" rather than "@". > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) > > Peter You have to be using a version of BioPerl that supports this. The previous version of the FASTQ parser released prior to refactoring returned FASTA when using write_seq(), which was a significant bug that was fixed during the complete overhaul prior to the FASTQ paper. My guess is the version of BioPerl is old and this is the module version being used. chris PS - Peter, had several very good mentions of this work from all Bio*/EMBOSS talks at BOSC, so a great success! From abhishek.vit at gmail.com Sat Jul 10 16:38:06 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Sat, 10 Jul 2010 16:38:06 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: Thanks guys. Time to update my Bioperl. I will do that and report if I face issues. -A On Sat, Jul 10, 2010 at 3:23 PM, Chris Fields wrote: > On Jul 10, 2010, at 6:44 AM, Peter wrote: > > > On Sat, Jul 10, 2010 at 12:43 PM, Peter > wrote: > >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap > wrote: > >>> Hi (Chris) > >>> > >>> I feel I might be hitting a bug or missing something. I am trying to > convert > >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code > and IO > >>> for more clarity. I think the quality line is missing and the read is > >>> breaking into two lines. > >>> > >>> Any obvious mistakes ? > >>> > >>> Thanks! > >>> -Abhi > >> > >> It looks like you are getting FASTQ out rather than FASTQ (notice in > addition to > >> missing the qualities, the record starts with ">" rather than "@". > > > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close > together ;) > > > > Peter > > You have to be using a version of BioPerl that supports this. The previous > version of the FASTQ parser released prior to refactoring returned FASTA > when using write_seq(), which was a significant bug that was fixed during > the complete overhaul prior to the FASTQ paper. My guess is the version of > BioPerl is old and this is the module version being used. > > chris > > PS - Peter, had several very good mentions of this work from all > Bio*/EMBOSS talks at BOSC, so a great success! From pengyu.ut at gmail.com Sat Jul 10 21:40:47 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sat, 10 Jul 2010 20:40:47 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) Message-ID: Hi, I have the following warnings and perl program. I don't understand why there is a warning and what the error is. The ncbi's eutils url seems OK. If shrink $term (see the code), then the warning is gone. Could somebody let me know what the problem is with my bioperl code? http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 $ ./main.pl |head --------------------- WARNING --------------------- MSG: NCBI esearch Errors/Warnings: Error : --------------------------------------------------- 241 2412410 20616305 20581223 20572313 20564721 20554763 20542744 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::DB::EUtilities; my $factory = Bio::DB::EUtilities->new( -eutil => 'esearch', -db => 'pubmed', -email => 'mymail at foo.bar', #-term => 'anoxia[mh] AND neoplasms[mh]', #-term => 'small ubiquitin-related modifier proteins[mh]', -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR hCaCC-1[tiab]', #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink $term, then the warning is gone. -retmode => 'xml', -retmax => 1000000, ); print $factory->get_retmax,"\n"; print $factory->get_Response->content; -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 11:14:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 10:14:54 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: Message-ID: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > Hi, > > I have the following warnings and perl program. I don't understand why > there is a warning and what the error is. The ncbi's eutils url seems > OK. If shrink $term (see the code), then the warning is gone. Could > somebody let me know what the problem is with my bioperl code? > > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 > > $ ./main.pl |head > > --------------------- WARNING --------------------- > MSG: NCBI esearch Errors/Warnings: > Error : > --------------------------------------------------- > 241 > > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> > 2412410 > 20616305 > 20581223 > 20572313 > 20564721 > 20554763 > 20542744 > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::DB::EUtilities; > > my $factory = Bio::DB::EUtilities->new( > -eutil => 'esearch', > -db => 'pubmed', > -email => 'mymail at foo.bar', > #-term => 'anoxia[mh] AND neoplasms[mh]', > #-term => 'small ubiquitin-related modifier proteins[mh]', > -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] > OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR > hCaCC-1[tiab]', > #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink > $term, then the warning is gone. > -retmode => 'xml', > -retmax => 1000000, > ); > > print $factory->get_retmax,"\n"; > print $factory->get_Response->content; > > > -- > Regards, > Peng The above XML output from that query isn't complete; you left out: CLCRG1[tiab]FLJ95147[tiab] It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. I can take a look, but the error is pretty obvious from that output (can't find those phrases). chris From pengyu.ut at gmail.com Sun Jul 11 15:54:20 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 14:54:20 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 10:14 AM, Chris Fields wrote: > On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > >> Hi, >> >> I have the following warnings and perl program. I don't understand why >> there is a warning and what the error is. The ncbi's eutils url seems >> OK. If shrink $term (see the code), then the warning is gone. Could >> somebody let me know what the problem is with my bioperl code? >> >> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 >> >> $ ./main.pl |head >> >> --------------------- WARNING --------------------- >> MSG: NCBI esearch Errors/Warnings: >> Error : >> --------------------------------------------------- >> 241 >> >> > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> >> 2412410 >> ? ? ? ? ? ? ? 20616305 >> ? ? ? ? ? ? ? 20581223 >> ? ? ? ? ? ? ? 20572313 >> ? ? ? ? ? ? ? 20564721 >> ? ? ? ? ? ? ? 20554763 >> ? ? ? ? ? ? ? 20542744 >> $ cat main.pl >> #!/usr/bin/env perl >> >> use strict; >> use warnings; >> use Bio::DB::EUtilities; >> >> my $factory = Bio::DB::EUtilities->new( >> ?-eutil => 'esearch', >> ?-db => 'pubmed', >> ?-email => 'mymail at foo.bar', >> ?#-term => 'anoxia[mh] AND neoplasms[mh]', >> ?#-term => 'small ubiquitin-related modifier proteins[mh]', >> ?-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] >> OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR >> hCaCC-1[tiab]', >> ?#-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink >> $term, then the warning is gone. >> ?-retmode => 'xml', >> ?-retmax => 1000000, >> ); >> >> print $factory->get_retmax,"\n"; >> print $factory->get_Response->content; >> >> >> -- >> Regards, >> Peng > > The above XML output from that query isn't complete; you left out: > > CLCRG1[tiab]FLJ95147[tiab] > > It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. ?I can take a look, but the error is pretty obvious from that output (can't find those phrases). Is there a way to suppress such error and warning message as they are not interesting to me? (As I can always check how many pubmed ids returned to determine if the search results anything). -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 17:16:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 16:16:15 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > ... > Is there a way to suppress such error and warning message as they are > not interesting to me? (As I can always check how many pubmed ids > returned to determine if the search results anything). > > -- > Regards, > Peng Setting -verbose to -1 should work. chris From pengyu.ut at gmail.com Sun Jul 11 20:04:30 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 19:04:30 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > >> ... >> Is there a way to suppress such error and warning message as they are >> not interesting to me? (As I can always check how many pubmed ids >> returned to determine if the search results anything). >> >> -- >> Regards, >> Peng > > Setting -verbose to -1 should work. I don't see such an option in perldoc Bio::DB::EUtilities. Would you please let me know where it is documented? In fact, I don't see the document for new() in Bio::DB::EUtilities. Would you please add this to the document? Thank you! -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 20:49:37 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 19:49:37 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <98EC5021-C5BC-4568-8080-99AC1C0C95A1@illinois.edu> On Jul 11, 2010, at 7:04 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: >> >> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: >> >>> ... >>> Is there a way to suppress such error and warning message as they are >>> not interesting to me? (As I can always check how many pubmed ids >>> returned to determine if the search results anything). >>> >>> -- >>> Regards, >>> Peng >> >> Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng verbose() is a Bio::Root::Root/RootI method (all BioPerl classes inherit it), so that's the place to look. As for new(), yes I can work on that. chris From Russell.Smithies at agresearch.co.nz Sun Jul 11 21:08:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 13:08:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Take a look at the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities Details all the methods including those that are inherited. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peng Yu > Sent: Monday, 12 July 2010 12:05 p.m. > To: Chris Fields > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields > wrote: > > > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > > > >> ... > >> Is there a way to suppress such error and warning message as they are > >> not interesting to me? (As I can always check how many pubmed ids > >> returned to determine if the search results anything). > >> > >> -- > >> Regards, > >> Peng > > > > Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng > _______________________________________________ > 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 pengyu.ut at gmail.com Sun Jul 11 21:15:46 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 20:15:46 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell wrote: > Take a look at the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > > Details all the methods including those that are inherited. This is every useful when l look for an inherent method. The box titled "methods for Bio::DB::EUtilities" is too small. May I suggest to make it a little bigger? Also, the box above it takes too much space, it is better to shrink it since there in only one class. Would you please help improve the appearance a little? -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 23:45:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 22:45:48 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > wrote: >> Take a look at the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities >> >> Details all the methods including those that are inherited. > > This is every useful when l look for an inherent method. The box > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > to make it a little bigger? Also, the box above it takes too much > space, it is better to shrink it since there in only one class. Would > you please help improve the appearance a little? > > -- > Regards, > Peng Patches welcome chris From Russell.Smithies at agresearch.co.nz Mon Jul 12 00:07:28 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:07:28 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> I think you mean "on your PC the box is too small". Because BioPerl is cross-platform it shouldn't be customized to look best on specific hardware or software , for example, Windows 7 with IE9. The Deobfuscator is included in BioPerl so you are free to edit and run on your own web-server with colors and styles to suit your exacting tastes. And as Chris said, if you'd like added documentation or a web interface changed so it looks better on your PC I suggest you start writing some patches. Don't forget, the BioPerl developers are all volunteers and don't work for you!! --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Monday, 12 July 2010 3:46 p.m. > To: Peng Yu > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > > > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > > wrote: > >> Take a look at the deobfuscator: > >> http://bioperl.org/cgi- > bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&so > rt_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > >> > >> Details all the methods including those that are inherited. > > > > This is every useful when l look for an inherent method. The box > > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > > to make it a little bigger? Also, the box above it takes too much > > space, it is better to shrink it since there in only one class. Would > > you please help improve the appearance a little? > > > > -- > > Regards, > > Peng > > Patches welcome > > chris ======================================================================= 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 Russell.Smithies at agresearch.co.nz Mon Jul 12 00:27:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:27:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347F6@exchsth.agresearch.co.nz> It's all a matter of priorities and I can't see how increasing the number of rows displayed in a web interface is more important than any other items on the list http://www.bioperl.org/wiki/Project_priority_list If you feel strongly about it and you can justify the changes then submit a bug report, and a patch. --Russell > -----Original Message----- > From: Peng Yu [mailto:pengyu.ut at gmail.com] > Sent: Monday, 12 July 2010 4:15 p.m. > To: Smithies, Russell > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 11:07 PM, Smithies, Russell > wrote: > > I think you mean "on your PC the box is too small". > > Because BioPerl is cross-platform it shouldn't be customized to look > best on specific hardware or software , for example, Windows 7 with IE9. > > The Deobfuscator is included in BioPerl so you are free to edit and run > on your own web-server with colors and styles to suit your exacting > tastes. > > > > And as Chris said, if you'd like added documentation or a web interface > changed so it looks better on your PC I suggest you start writing some > patches. > > Don't forget, the BioPerl developers are all volunteers and don't work > for you!! > > This is just a suggestion. Do you think that this is an order? I > didn't mean so. My believe is that if I feel something can be > improved, maybe others think so as well. So I'm make the suggestions > for other users as well. > > You don't have to reply if it can not be done. > > -- > Regards, > Peng ======================================================================= 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 dan.bolser at gmail.com Mon Jul 12 05:34:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 10:34:47 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: OK, here is my final version. I have tested it with GFF / Fasta, and in theory it works with all installed BioPerl sequence / feature file formats, however, I haven't tested any of those. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $feature_file; my $sequence_file; my $feature_format = 'GFF'; my $sequence_format = 'Fasta'; my $feature_to_mask = 'repeat_region'; my $seq_mask_character = 'X'; GetOptions ( "verbose" => \$verbose, "feature_file|f=s" => \$feature_file, "sequence_file|s=s" => \$sequence_file, "feature_format|ff=s" => \$feature_format, "sequence_format|sf=s" => \$sequence_format, "feature_to_mask|m=s" => \$feature_to_mask, "seq_mask_character|c=s" => \$seq_mask_character, ) or die "failed to parse command line options\n"; ## Check options ## A value should be passed die usage() unless $sequence_file && $feature_file; ## The files should exist die "problem with feature file '$feature_file' : $!\n" unless -s $feature_file; die "problem with sequence file '$sequence_file' : $!\n" unless -s $sequence_file; ## The formats should be valid $feature_format = lc($feature_format); die "ERROR: feature format '$feature_format' is not supported!\n\n" unless eval( "require Bio::FeatureIO::$feature_format" ); $sequence_format = lc($sequence_format); die "ERROR: sequence format '$sequence_format' is not supported!\n\n" unless eval( "require Bio::SeqIO::$sequence_format" ); ## Erm... die "1: what are you trying to do?\n" unless $feature_to_mask; die "2: what are you trying to do?\n" unless length($seq_mask_character) == 1; =head1 NAME bp_repeat_mask_sequence.pl - mask sequence features =head1 DESCRIPTION Takes an input sequence file and a feature file, and returns the sequence with 'repeat_region' features masked out (replaced with X's). This is useful for downstream processing of the sequence file. The masked sequence is written to STDOUT. =head1 USAGE bp_repeat_mask_sequence.pl Options: -f --feature_file The file from which the sequence features will be read (for subsequent masking). -s --sequence_file The sequence file (to be masked). --ff --feature_format The format of the feature file (the default is GFF). --sf --sequence_format The format of the sequence file (the default is fasta). -m --feature_to_mask The type of feature to mask (the default is 'repeat_region'). -c --seq_mask_character The 'mask' character to use in the sequence. (the default is 'X'). -v --verbose Generate some debugging output =cut ## Set up the BioPerl objects my $gff_reader = Bio::FeatureIO->new( -file => $feature_file, -format => $feature_format ); my $seq_reader = Bio::SeqIO->new( -file => $sequence_file, -format => $sequence_format, ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => $sequence_format, ); ## Run warn "hashing features to mask\n"; my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>0){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq $feature_to_mask){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } } warn "read $c '$feature_to_mask' features for ", scalar keys(%repeats), " sequences\n"; warn "masking sequences\n"; while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; ## Do the masking for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, $seq_mask_character x ($end - $start) ); } $seq->seq($sequence); $seq_writer->write_seq($seq); } warn "done\n"; # A bit of a hack: sub usage{ `perldoc -T ./$0` } On 7 July 2010 10:42, Brian Osborne wrote: > Dan, > > In my opinion the user should be able to use any supported format as input, yes. > > Brian O. > > On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > >> Cheers Brian! >> >> Do you think this script will work if I allow sequence and feature >> '-format's to be picked by the user among all those listed as valid >> file formats in BioPerl? >> >> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats >> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS >> >> >> Or should I stick to Fasta/GFF (or some other implementation)? >> >> Cheers, >> Dan. >> >> >> On 6 July 2010 15:50, Brian Osborne wrote: >>> Dan, >>> >>> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >>> >>> =head1 NAME >>> >>> bioflat_index.pl - index sequence files using Bio::DB::Flat >>> >>> =head1 DESCRIPTION >>> >>> Create or update a biological sequence database indexed with the >>> Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files >>> containing the sequence information to be indexed. >>> >>> =head1 USAGE >>> >>> bioflat_index.pl file1 file2 file3... >>> >>> Options: >>> >>> ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, >>> ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. >>> >>> ? --format ? ? The format of the sequence files. ?Must be one >>> ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". >>> >>> ? --location ? ? Path to the directory in which the index files >>> ? ? ? ? ? ? ? ? ? ? ? ? are stored. >>> >>> ? --dbname ? ? ? The symbolic name of the database to be created. >>> >>> ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". >>> ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". >>> >>> Options can be abbreviated. ?For example, use -i for --indextype. >>> >>> The following environment variables will be used as defaults if the >>> corresponding options are not provided: >>> >>> ? OBDA_FORMAT ? ? ?format of sequence file >>> ? OBDA_LOCATION ? ?path to directory in which index files are stored >>> ? OBDA_DBNAME ? ? ?name of database >>> ? OBDA_INDEX ? ? ? type of index to create >>> >>> =cut >>> >>> >>> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >>> >>>> Hello, >>>> >>>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>>> set of scripts in BioPerl. Below is what I have so far. The script >>>> works by reading in a GFF of 'repeat_region's and a fasta file of >>>> sequences. It outputs a fasta sequence file with the repeats replaced >>>> by Xs. >>>> >>>> The script clearly needs to be more configurable, but I thought I'd >>>> send it along now to see if I'm working along the right lines, or if I >>>> should be using a different approach. >>>> >>>> Comments? >>>> >>>> >>>> Cheers, >>>> Dan. >>>> >>>> >>>> >>>> #!/usr/bin/perl -w >>>> >>>> use strict; >>>> use Getopt::Long; >>>> >>>> use Bio::SeqIO; >>>> use Bio::FeatureIO; >>>> >>>> >>>> >>>> ## Set options >>>> >>>> my $verbose = 0; >>>> my $seq_file; >>>> my $gff_file; >>>> >>>> GetOptions >>>> ( >>>> "verbose" => \$verbose, >>>> "seq=s" => \$seq_file, >>>> "gff=s" => \$gff_file, >>>> ) >>>> or die "failed to parse command line options\n"; >>>> >>>> die "fail $gff_file : $!\n" >>>> unless -s $gff_file; >>>> >>>> >>>> >>>> ## Set up the BioPerl objects >>>> >>>> my $seq_reader = >>>> Bio::SeqIO->new( -file => $seq_file, >>>> ? ? ? ? ? ? ? ?-format => 'fasta' >>>> ? ? ? ? ? ? ?); >>>> >>>> my $seq_writer = >>>> Bio::SeqIO->new( -fh => \*STDOUT, >>>> ? ? ? ? ? ? ? ?-format => 'fasta', >>>> ? ? ? ? ? ? ? ?-width => 80 >>>> ? ? ? ? ? ? ?); >>>> >>>> my $gff_reader = >>>> Bio::FeatureIO->new( -file => $gff_file, >>>> ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >>>> ? ? ? ? ? ? ? ? ?); >>>> >>>> #warn $seq_reader->width, "\n"; exit; >>>> >>>> >>>> >>>> ## Run >>>> >>>> my (%repeats, $c); >>>> >>>> while ( my $feature = $gff_reader->next_feature() ) { >>>> if($verbose>1){ >>>> ?print >>>> ? ?join("\t", #$feature, >>>> ? ? ? ?$feature->seq_id, >>>> ? ? ? ?$feature->type->name, >>>> ? ? ? ?$feature->start, >>>> ? ? ? ?$feature->end, >>>> ? ? ? ), "\n"; >>>> } >>>> >>>> if($feature->type->name eq 'repeat_region'){ >>>> ?$c++; >>>> ?push @{$repeats{ $feature->seq_id }}, >>>> ? ?[$feature->start, >>>> ? ? $feature->end]; >>>> } >>>> >>>> # Debugging >>>> #last if $c > 100; >>>> } >>>> >>>> warn "read $c repeat_region features for ", >>>> scalar keys(%repeats), " sequences\n"; >>>> >>>> >>>> >>>> ## >>>> >>>> while(my $seq = $seq_reader->next_seq){ >>>> my $id = $seq->id; >>>> my $sequence = $seq->seq; >>>> >>>> print $id, "\n" >>>> ?if $verbose > 0; >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> for my $region (@{$repeats{ $id }}){ >>>> ?my ($start, $end) = @$region; >>>> ?print "$start\t$end\n" >>>> ? ?if $verbose > 1; >>>> >>>> ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>>> } >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> $seq->seq($sequence); >>>> >>>> $seq_writer->write_seq($seq); >>>> >>>> # Debugging; >>>> #last; >>>> } >>>> >>>> warn "OK\n"; >>>> _______________________________________________ >>>> 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 Jul 12 08:42:58 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 13:42:58 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" Message-ID: Seems I still can't log bugs here: https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 Error: Artifact: Only Artifact Admins Can Modify Private ArtifactTypes Here I my bug report: I'm following the tutorial here: http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html I successfully set up and browsed the first database (going no further than #data_file). I decided to try switching from an in memory (file-based) database to a DBI::mysql database. After taking the appropriate steps (see below), I get the following error when viewing the database in GB: The landmark named ctgA is not recognized. See the help pages for suggestions. I'm not sure why the landmark is found using a memory (file-based) database, but not found when using the same GFF loaded into mysql. This is the latest bioperl-live (although I'm still struggling with git). Any hints on what might be going wrong? I've a feeling I should perhaps roll back a few versions, as I noticed some SQL errors coming from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". Cheers, Dan. 1) I loaded the GFF: bp_seqfeature_load.pl -v -v -f -c -z \ --dsn dbi:mysql:mydb:myhost \ --namespace volvox \ --summary \ -u me -p secret \ databases/volvox/volvox_remarks.gff3 2) I changed the volvox.conf file: #db_args = -adaptor memory # -dir '$HTDOCS/databases/volvox' db_args = -adaptor DBI::mysql -dsn mydb:myhost -namespace volvox -user me -pass secret From shalabh.sharma7 at gmail.com Mon Jul 12 10:56:56 2010 From: shalabh.sharma7 at gmail.com (shalabh sharma) Date: Mon, 12 Jul 2010 10:56:56 -0400 Subject: [Bioperl-l] Intergenic regions Message-ID: Hi All, I am trying to find intergenic regions/sequences in genomes. Is there any bioperl module for that ? or any other package/software available? I would really appreciate if anyone can help me out. Thanks Shalabh From awitney at sgul.ac.uk Mon Jul 12 11:37:05 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Mon, 12 Jul 2010 16:37:05 +0100 Subject: [Bioperl-l] Intergenic regions In-Reply-To: References: Message-ID: If the genomes are already annotated then I guess you could just the Bio::Seq modules to pull out the intergenic regions. If there is no annotation yet then you would need to run some kind of gene prediction software first eg Genescan, Glimmer (google will throw up several choices). cheers adam On 12 Jul 2010, at 15:56, shalabh sharma wrote: > Hi All, > I am trying to find intergenic regions/sequences in genomes. Is > there any bioperl module for that ? or any other package/software available? > > I would really appreciate if anyone can help me out. > > Thanks > Shalabh > _______________________________________________ > 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 Jul 12 12:56:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 12 Jul 2010 11:56:12 -0500 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: Message-ID: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Dan. Is this maybe something for the GBrowse list? (cc'ing there JIC) chris On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > --dsn dbi:mysql:mydb:myhost \ > --namespace volvox \ > --summary \ > -u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args = -adaptor memory > # -dir '$HTDOCS/databases/volvox' > > db_args = -adaptor DBI::mysql > -dsn mydb:myhost > -namespace volvox > -user me > -pass secret > _______________________________________________ > 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 Tue Jul 13 03:49:44 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 08:49:44 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: Cheers Chris, Is there a known good version of "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? I believe that this is one of the more common databases, so I'm surprised to find it broken. What would be the git command to roll back to a stable BioPerl / GBrowse? Sorry for the basic questions, Dan. On 12 July 2010 17:56, Chris Fields wrote: > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From mark.alston at BBSRC.AC.UK Tue Jul 13 06:47:04 2010 From: mark.alston at BBSRC.AC.UK (mark alston (TGAC)) Date: Tue, 13 Jul 2010 11:47:04 +0100 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... Message-ID: Hi, BioPerl newbie question coming up... I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. Here's my script after days of effort (I joke not): ######################################################################### use Bio::DB::Taxonomy ; my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects foreach my $nodelet (@taxa) { print $nodelet->to_string() . "\t" ; } ######################################################################### This outputs: 131567 2 1224 1236 91347 543 413496 28141 290339 If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because 2 corresponds to: bacteria (superkingdom) 1224 corresponds to: proteobacteria (phylum) etc etc 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) But how can I get the things I've underlined out via BioPerl? Many thanks, Mark ################################################ Dr Mark Alston, Computer Biologist, The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK. tel +44 (0)1603 450910 e-mail mark.alston at bbsrc.ac.uk web http://www.tgac.bbsrc.ac.uk ################################################ From cjfields at illinois.edu Tue Jul 13 08:58:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jul 2010 07:58:41 -0500 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... In-Reply-To: References: Message-ID: Change to the following: { print $nodelet->scientific_name() . "\t" ; } chris On Jul 13, 2010, at 5:47 AM, mark alston (TGAC) wrote: > Hi, > BioPerl newbie question coming up... > I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. > Here's my script after days of effort (I joke not): > ######################################################################### > use Bio::DB::Taxonomy ; > my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); > > my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; > my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; > > my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects > > foreach my $nodelet (@taxa) > { print $nodelet->to_string() . "\t" ; } > ######################################################################### > > This outputs: > 131567 2 1224 1236 91347 543 413496 28141 290339 > > If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because > 2 corresponds to: bacteria (superkingdom) > 1224 corresponds to: proteobacteria (phylum) > etc etc > 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) > > > But how can I get the things I've underlined out via BioPerl? > Many thanks, > Mark > > ################################################ > Dr Mark Alston, > Computer Biologist, > The Genome Analysis Centre, > Norwich Research Park, > Colney Lane, Norwich, NR4 7UH, UK. > > tel +44 (0)1603 450910 > e-mail mark.alston at bbsrc.ac.uk > web http://www.tgac.bbsrc.ac.uk > ################################################ > > > _______________________________________________ > 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 Tue Jul 13 13:15:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 18:15:02 +0100 Subject: [Bioperl-l] Coordinate converter? Message-ID: Hi, When one sequence exists in the context of another larger sequence (with a precise start, end and strand), what is the easiest way to convert coordinates between the two sequences? I'm guessing there is an object I can load with the appropriate information with a conversion method? However, I'm stuck for details. I have implemented sub-sequences as features, but I'm not sure what to do next. Thanks for any hints, Dan. irc://irc.freenode.net/#bioperl From armendarez77 at hotmail.com Tue Jul 13 14:00:27 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:00:27 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Message-ID: Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From randalls at bioinfo.wsu.edu Tue Jul 13 14:43:35 2010 From: randalls at bioinfo.wsu.edu (randalls at bioinfo.wsu.edu) Date: Tue, 13 Jul 2010 11:43:35 -0700 (PDT) Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: Message-ID: <108709378.25.1279046615031.JavaMail.root@mail> One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Tue Jul 13 14:38:24 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 13 Jul 2010 11:38:24 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <1A4207F8295607498283FE9E93B775B406D676E9@EX02.asurite.ad.asu.edu> And a 64-bit OS and program to be able to utilize greater than 3GB of RAM. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of randalls at bioinfo.wsu.edu Sent: Tuesday, July 13, 2010 11:44 AM To: armendarez77 at hotmail.com Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PI D28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 13 14:57:54 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:57:54 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: That would be nice, but not possible right now :) > Date: Tue, 13 Jul 2010 11:43:35 -0700 > From: randalls at bioinfo.wsu.edu > To: armendarez77 at hotmail.com > CC: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation > > One suggestion is to use a computer with a lot more memory...... > > Randall Svancara > Systems Administrator/DBA/Developer > Main Bioinformatics Laboratory > > > > ----- Original Message ----- > From: armendarez77 at hotmail.com > To: bioperl-l at lists.open-bio.org > Sent: Tuesday, July 13, 2010 11:00:27 AM > Subject: [Bioperl-l] Muscle Alignment and Memory Allocation > > Hello, > > I need to align 20-30 large full genome sequences (150,000+ bp each), > but I run out of memory. I've tried using -maxmb at the command line and > as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either > using it wrong or it's not working. > > I've also tried aligning 2 sequences at a time and then aligning those > alignments using the -profile command, but it's still too much. > > Do you have any advice on how to do such alignments? My attempts are > below. > > Thank you, > > Veronica > > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB > > Alignment not completed, cannot save. > > > > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout > 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.74 MB > > Alignment not completed, cannot save. > > > Using Bio::Tools::Run::Alignment::Muscle and -maxmb > > SCRIPT: my $inputFile = $ARGV[0]; > my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); > > my $alnObj = $factory->align($inputFile); > my $output = "output.clw"; > my $clwOut = Bio::AlignIO->new(-format=>'clustalw', > -file=>">$output.clw"); $clwOut->write_aln($alnObj); > > OUTPUT: > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.9 MB > > Alignment not completed, cannot save. > > --------------------- WARNING --------------------- > MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in > 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] > > --------------------------------------------------- > > > > > > > _________________________________________________________________ The > New Busy is not the too busy. Combine all your e-mail accounts with > Hotmail. > http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 > _______________________________________________ Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From David.Messina at sbc.su.se Tue Jul 13 15:05:16 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jul 2010 15:05:16 -0400 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4B92E3EE-1001-44EE-8D78-B3B05E78A13E@sbc.su.se> I would contact the MUSCLE authors to see what they say, but like Randall said I would suspect that you won't be able to do such a large multiple alignment in 4GB of RAM. Dave From kai.blin at biotech.uni-tuebingen.de Tue Jul 13 14:42:58 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Tue, 13 Jul 2010 20:42:58 +0200 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: Message-ID: <1279046578.2560.14.camel@gonzo.home.kblin.org> On Tue, 2010-07-13 at 11:00 -0700, armendarez77 at hotmail.com wrote: Hi Veronica, > I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. The fact that this also fails on the command line tells me that you're not running into a BioPerl problem. See my comments inline below: [...] > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB ^^^^^^^^^^ [...] > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 ^^^^^^^^^^^^ You're running out of memory at 3211.48 MB, but you're telling muscle it's fine to use 4000 MB. Maybe you might want to provide less memory to -maxmb ..... Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From jason at bioperl.org Tue Jul 13 18:41:24 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:41:24 -0700 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: Message-ID: <4C3CEB94.300@bioperl.org> Bio::Coordinate::Pair? Dan Bolser wrote, On 7/13/10 10:15 AM: > Hi, > > When one sequence exists in the context of another larger sequence > (with a precise start, end and strand), what is the easiest way to > convert coordinates between the two sequences? > > I'm guessing there is an object I can load with the appropriate > information with a conversion method? However, I'm stuck for details. > > I have implemented sub-sequences as features, but I'm not sure what to do next. > > Thanks for any hints, > Dan. > > > irc://irc.freenode.net/#bioperl > _______________________________________________ > 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 Tue Jul 13 18:44:32 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:44:32 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4C3CEC50.6010102@bioperl.org> Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: > That would be nice, but not possible right now :) > > > > >> Date: Tue, 13 Jul 2010 11:43:35 -0700 >> From: randalls at bioinfo.wsu.edu >> To: armendarez77 at hotmail.com >> CC: bioperl-l at lists.open-bio.org >> Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> One suggestion is to use a computer with a lot more memory...... >> >> Randall Svancara >> Systems Administrator/DBA/Developer >> Main Bioinformatics Laboratory >> >> >> >> ----- Original Message ----- >> From: armendarez77 at hotmail.com >> To: bioperl-l at lists.open-bio.org >> Sent: Tuesday, July 13, 2010 11:00:27 AM >> Subject: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> Hello, >> >> I need to align 20-30 large full genome sequences (150,000+ bp each), >> but I run out of memory. I've tried using -maxmb at the command line and >> as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either >> using it wrong or it's not working. >> >> I've also tried aligning 2 sequences at a time and then aligning those >> alignments using the -profile command, but it's still too much. >> >> Do you have any advice on how to do such alignments? My attempts are >> below. >> >> Thank you, >> >> Veronica >> >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3211.48 MB >> >> Alignment not completed, cannot save. >> >> >> >> Using -maxmb at the command line: >> >> $ muscle -in 07-13-2010_fullGenomes.fasta -clwout >> 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.74 MB >> >> Alignment not completed, cannot save. >> >> >> Using Bio::Tools::Run::Alignment::Muscle and -maxmb >> >> SCRIPT: my $inputFile = $ARGV[0]; >> my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); >> >> my $alnObj = $factory->align($inputFile); >> my $output = "output.clw"; >> my $clwOut = Bio::AlignIO->new(-format=>'clustalw', >> -file=>">$output.clw"); $clwOut->write_aln($alnObj); >> >> OUTPUT: >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.9 MB >> >> Alignment not completed, cannot save. >> >> --------------------- WARNING --------------------- >> MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in >> 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] >> >> --------------------------------------------------- >> >> >> >> >> >> >> _________________________________________________________________ The >> New Busy is not the too busy. Combine all your e-mail accounts with >> Hotmail. >> http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 >> _______________________________________________ Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 13 18:48:20 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:48:20 -0700 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: <4C3CED34.9050607@bioperl.org> Dan - I'm not convinced that contig:example is proper type/source for the landmarks & scaffold - i use 'scaffold:chromosome' in my data: What happens if you change the GFF3 file line from ctgA example contig 1 50000 . . . Name=ctgA to ctgA chromosome scaffold 1 50000 . . . Name=ctgA I think this can be tweaked in the config but there may be different defaults for the in memory and DBI::mysql implementation. -jason Dan Bolser wrote, On 7/13/10 12:49 AM: > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >>> Seems I still can't log bugs here: >>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >>> >>> Error: >>> Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >>> >>> >>> Here I my bug report: >>> >>> I'm following the tutorial here: >>> >>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >>> >>> >>> I successfully set up and browsed the first database (going no further >>> than #data_file). I decided to try switching from an in memory >>> (file-based) database to a DBI::mysql database. After taking the >>> appropriate steps (see below), I get the following error when viewing >>> the database in GB: >>> >>> The landmark named ctgA is not recognized. See the help pages >>> for suggestions. >>> >>> >>> I'm not sure why the landmark is found using a memory (file-based) >>> database, but not found when using the same GFF loaded into mysql. >>> >>> This is the latest bioperl-live (although I'm still struggling with git). >>> >>> Any hints on what might be going wrong? I've a feeling I should >>> perhaps roll back a few versions, as I noticed some SQL errors coming >>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> 1) I loaded the GFF: >>> >>> bp_seqfeature_load.pl -v -v -f -c -z \ >>> --dsn dbi:mysql:mydb:myhost \ >>> --namespace volvox \ >>> --summary \ >>> -u me -p secret \ >>> databases/volvox/volvox_remarks.gff3 >>> >>> >>> 2) I changed the volvox.conf file: >>> >>> #db_args = -adaptor memory >>> # -dir '$HTDOCS/databases/volvox' >>> >>> db_args = -adaptor DBI::mysql >>> -dsn mydb:myhost >>> -namespace volvox >>> -user me >>> -pass secret >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 03:38:04 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 09:38:04 +0200 Subject: [Bioperl-l] getting only the aminoacids for a domain Message-ID: Hi, with these lines I download protein sequences matching "jjjj" uniprot code. !/usr/bin/perl use lib '/sw/share/bioperl-pm588'; use Bio::SeqIO; use Bio::DB::SwissProt; $db_obj = Bio::DB::SwissProt->new; $seq_obj = $db_obj->get_Seq_by_id('jjjj'); ...from here, I cut the sequences and get only a piece of each one (with subseq, between j1 and j2 residues) $shortened = $seq_obj->subseq(j1,j2); $seq_obj->seq($shortened); $seqio_obj = Bio::SeqIO->new(-file => '>jjjj.jletra.j1_j2.fasta', -format => 'fasta' ); $seqio_obj->write_seq($seq_obj); How can I download the sequence of ONLY THOSE AMINOACIDS that match, in uniprot, in the Sequence annotation section, Feature key: Domain & Description: lectin, ANK, Sushi,... the name of a given domain ? Is there any way of downloading all the existing fasta sequences for a given domain? Thanks in advance, JR From dan.bolser at gmail.com Wed Jul 14 06:27:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 11:27:02 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <4C3CED34.9050607@bioperl.org> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: Hi Jason, Thanks for the suggestion (see below). On 13 July 2010 23:48, Jason Stajich wrote: > Dan - > I'm not convinced that contig:example is proper type/source for the > landmarks & scaffold - i use 'scaffold:chromosome' in my data: > > What happens if you change the GFF3 file line from > ctgA example contig 1 50000 . . . Name=ctgA > to > ctgA chromosome scaffold 1 50000 . . . Name=ctgA > > > I think this can be tweaked in the config but there may be different > defaults for the in memory and DBI::mysql implementation. I found that this doesn't make any difference, however, I have found more information about what causes the bug. >From my previous email you see that I use bp_seqfeature_load.pl with the "--namespace volvox" option (I should have guessed it was something to do with this). Looking closely at the resulting tables I see that the following tables are empty volvox_attribute volvox_parent2child volvox_feature volvox_interval_stats volvox_name volvox_parent2child they are not empty when created without the "--namespace x" prefix, which is why DBI::mysql 'normally' works. All the other tables: volvox_attributelist volvox_locationlist volvox_meta volvox_sequence volvox_typelist appear to be created correctly, with or without the "--namespace x" prefix. Cheers, Dan. > -jason > Dan Bolser wrote, On 7/13/10 12:49 AM: > > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > > > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > > > > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > ? ? ? ?The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > ?--dsn dbi:mysql:mydb:myhost \ > ?--namespace volvox \ > --summary \ > ?-u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args ? ? ? = -adaptor memory > # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' > > db_args ? ? ? = -adaptor DBI::mysql > ? ? ? ? ? ? ? ?-dsn mydb:myhost > ? ? ? ? ? ? ? ?-namespace volvox > ? ? ? ? ? ? ? ?-user me > ? ? ? ? ? ? ? ?-pass secret > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 06:35:17 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 12:35:17 +0200 Subject: [Bioperl-l] install cpan on mac os x Message-ID: Hi, I have found several problems when installing CPAN in Mac OS X (version 10.6.4) previous to install Bioperl. What's the best choice for installing Bioperl on Mac OS X? I had it installed by using fink, but several modules are not found, I prefer a Unix installation. Is there any trick that I have to bear in mind? Thanks, JR From awitney at sgul.ac.uk Wed Jul 14 08:09:33 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 13:09:33 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: Message-ID: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> I have always found the CPAN route the best way of installing BioPerl on OSX. If you are having problems doing this then try posting any errors and someone may be able to help adam On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > Hi, > I have found several problems when installing CPAN in Mac OS X (version > 10.6.4) previous to install Bioperl. > > What's the best choice for installing Bioperl on Mac OS X? I had it > installed by using fink, but several modules are not found, I prefer a Unix > installation. Is there any trick that I have to bear in mind? > > Thanks, > > JR > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From joseramonblas at gmail.com Wed Jul 14 09:29:53 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 15:29:53 +0200 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix When I do: >perl -MCPAN -e shell cpan> install Bundle::CPAN ...answer Yes to all... and the last lines of my installation are: t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 1. t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 255 tests but ran 2. Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) Result: FAIL Failed 67/85 test programs. 34/9260 subtests failed. make: *** [test_dynamic] Error 255 PMQS/IO-Compress-2.027.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports PMQS/IO-Compress-2.027.tar.gz Running make install make test had returned bad status, won't install without force Failed during this command: ADAMK/File-HomeDir-0.91.tar.gz : make_test NO PMQS/IO-Compress-2.027.tar.gz : make_test NO ...any hint on where my failure comes from is appreciated. More info: Mac OS X 10.4 Xcode developer tools installed Thanks, JR El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on > OSX. > > If you are having problems doing this then try posting any errors and > someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a > Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Jul 14 09:36:45 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 14:36:45 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: <74C17C09-7818-45C9-BD7C-896A74D37F17@sgul.ac.uk> looks like its failing to install PMQS/IO-Compress-2.027.tar.gz. Try installing it on its own cpan> install PMQS/IO-Compress-2.027.tar.gz On 14 Jul 2010, at 14:29, Jos? Ram?n Blas Pastor wrote: > I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > > When I do: > >perl -MCPAN -e shell > cpan> install Bundle::CPAN > > ...answer Yes to all... and the last lines of my installation are: > > t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) > Non-zero exit status: 255 > Parse errors: No plan found in TAP output > t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 29 tests but ran 1. > t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 255 tests but ran 2. > Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) > Result: FAIL > Failed 67/85 test programs. 34/9260 subtests failed. > make: *** [test_dynamic] Error 255 > PMQS/IO-Compress-2.027.tar.gz > /usr/bin/make test -- NOT OK > //hint// to see the cpan-testers results for installing this module, try: > reports PMQS/IO-Compress-2.027.tar.gz > Running make install > make test had returned bad status, won't install without force > Failed during this command: > ADAMK/File-HomeDir-0.91.tar.gz : make_test NO > PMQS/IO-Compress-2.027.tar.gz : make_test NO > > ...any hint on where my failure comes from is appreciated. > > More info: > Mac OS X 10.4 > Xcode developer tools installed > > Thanks, > > JR > > El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on OSX. > > If you are having problems doing this then try posting any errors and someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Wed Jul 14 12:33:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 17:33:47 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <4C3CEB94.300@bioperl.org> References: <4C3CEB94.300@bioperl.org> Message-ID: Brilliant! Thanks Jason. I found the example in the docs a bit confusing, so here is my version (hopefully to be built into an AGP object): #!/usr/bin/perl -w use Bio::Location::Simple; use Bio::Coordinate::Pair; my $ctg = Bio::Location::Simple-> new( -seq_id => 'ctg', -start => 1, -end => 999, -strand => +1 ); my $ctg_on_chr = Bio::Location::Simple-> new( -seq_id => 'chr', -start => 2001, -end => 2999, -strand => -1 ); my $agp = Bio::Coordinate::Pair-> new( -in => $ctg, -out => $ctg_on_chr ); my $match_on_ctg = Bio::Location::Simple-> new( -seq_id => 'hit', -start => 25, -end => 125, -strand => +1 ); print_loc( $agp->map( $match_on_ctg ) ); which gives: "chr 2875 2975 -1" I know the algorithm is simple, but it's not so simple to type it out, base perfect and bug free every time you need it. Cheers, Dan. On 13 July 2010 23:41, Jason Stajich wrote: > Bio::Coordinate::Pair? > > > Dan Bolser wrote, On 7/13/10 10:15 AM: >> >> Hi, >> >> When one sequence exists in the context of another larger sequence >> (with a precise start, end and strand), what is the easiest way to >> convert coordinates between the two sequences? >> >> I'm guessing there is an object I can load with the appropriate >> information with a conversion method? However, I'm stuck for details. >> >> I have implemented sub-sequences as features, but I'm not sure what to do >> next. >> >> Thanks for any hints, >> Dan. >> >> >> irc://irc.freenode.net/#bioperl >> _______________________________________________ >> 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 Jul 14 15:12:20 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jul 2010 13:12:20 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> Message-ID: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> On Jul 14, 2010, at 10:33, Dan Bolser wrote: > I found the example in the docs a bit confusing, Hey Dan, Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Dave From dan.bolser at gmail.com Thu Jul 15 04:42:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 09:42:12 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: On 14 July 2010 20:12, Dave Messina wrote: > > > > > On Jul 14, 2010, at 10:33, Dan Bolser wrote: > >> I found the example in the docs a bit confusing, > > > Hey Dan, > > Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Sure thing Dave. The wiki is my preferred choice because it's easy for me to edit. However, having looked a git a bit, it seems like it should be easy for me to now mod the pod. I've put my code example with comments here: http://bioperl.org/wiki/Module:Bio::Coordinate::Pair One of the main reasons that I gave up editing the wiki is the very slow response time. I'm not sure what the bottleneck could be, but page loads, history checks, open for edits, and saves all take way longer than I'd like. This is especially frustrating when you want to make minor edits. (It may be worth noting that minor edits are the way wikis work [1]). This could be a good opportunity to spam the following conference: NETTAB 2010 - Workshop on biological wikis http://www.nettab.org/2010/ Thanks again for help, Dan. [1] http://www.parc.com/publication/1749/power-of-the-few-vs-wisdom-of-the-crowd.html > Dave > From David.Messina at sbc.su.se Thu Jul 15 10:59:43 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 15 Jul 2010 08:59:43 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> > I've put my code example with comments here: > > http://bioperl.org/wiki/Module:Bio::Coordinate::Pair Great, thanks. Much appreciated. > One of the main reasons that I gave up editing the wiki is the very > slow response time. Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > NETTAB 2010 - Workshop on biological wikis > http://www.nettab.org/2010/ Ah, Naples...love that city. If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. Dave From biopython at maubp.freeserve.co.uk Thu Jul 15 11:41:32 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 16:41:32 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Thu, Jul 15, 2010 at 3:59 PM, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. > BioPerl is a volunteer project and our hosting space is donated. > There were some zombie perl crontab processes were running - Mauricio has killed them and is looking at updating/fixing them. The wiki does seem faster now :) Peter From dan.bolser at gmail.com Thu Jul 15 13:46:45 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 18:46:45 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On 15 July 2010 15:59, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. How big is the wiki database? How about moving to http://bifx.org? >> NETTAB 2010 - Workshop on biological wikis >> http://www.nettab.org/2010/ > > Ah, Naples...love that city. > > If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. > > > Dave From jovel_juan at hotmail.com Thu Jul 15 13:53:04 2010 From: jovel_juan at hotmail.com (Juan Jovel) Date: Thu, 15 Jul 2010 17:53:04 +0000 Subject: [Bioperl-l] How to convert SFF into Fastq Message-ID: Hello! How can I convert a SFF file from 454 into a Fastq format? Thanks a lot! JUAN _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline From biopython at maubp.freeserve.co.uk Thu Jul 15 14:40:05 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 19:40:05 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: > > Hello! > > How can I convert a SFF file from 454 into a Fastq format? > > Thanks a lot! > > JUAN I am aware of three options, none of which use Perl, (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget which), to give you FASTA+QUAL, then using your tool of choice go to FASTQ (e.g. BioPerl). (2) Use the open source command line tool sff_extract (written in Python), it can do FASTA and QUAL, and I think there is an option for FASTQ too. http://bioinf.comav.upv.es/sff_extract/ (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. Things are more complex if you are working with paired end data... Peter From cjfields at illinois.edu Thu Jul 15 15:01:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:01:32 -0500 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Jul 15, 2010, at 12:46 PM, Dan Bolser wrote: > On 15 July 2010 15:59, Dave Messina wrote: >> >>> I've put my code example with comments here: >>> >>> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair >> >> Great, thanks. Much appreciated. >> >> >>> One of the main reasons that I gave up editing the wiki is the very >>> slow response time. >> >> Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > > How big is the wiki database? > > How about moving to http://bifx.org? Depends. We have talked about migrating most (all?) of the most significantly used parts (wiki, blogs) to other sources for a while. The GitHub move also played into that. But this would be a wider OBF-based issue, as it would also involve migrating other OBF-based wikis as well. chris From cjfields at illinois.edu Thu Jul 15 15:04:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:04:15 -0500 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Jul 15, 2010, at 1:40 PM, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter We are planning some tools for SFF work with BioPerl, possibly using BioLib's io_lib bindings. Much of this is to replace the legacy io_lib bindings from bioperl-ext, which is essentially dead at the moment. chris From armendarez77 at hotmail.com Thu Jul 15 15:20:43 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Thu, 15 Jul 2010 12:20:43 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <4C3CEC50.6010102@bioperl.org> References: , <108709378.25.1279046615031.JavaMail.root@mail> , <4C3CEC50.6010102@bioperl.org> Message-ID: Thank you. I'll look into those programs. Veronica Date: Tue, 13 Jul 2010 15:44:32 -0700 From: jason at bioperl.org To: armendarez77 at hotmail.com CC: randalls at bioinfo.wsu.edu; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: That would be nice, but not possible right now :) Date: Tue, 13 Jul 2010 11:43:35 -0700 From: randalls at bioinfo.wsu.edu To: armendarez77 at hotmail.com CC: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 From cjfields at illinois.edu Fri Jul 16 00:38:10 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 23:38:10 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release Message-ID: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> All, After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? chris From dan.bolser at gmail.com Fri Jul 16 03:59:01 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 16 Jul 2010 08:59:01 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: (In theory,) the list of tools that produce and consume SFF can be found here: http://seqwiki.org/SFF Currently listed (and not already mentioned) is: * http://seqwiki.org/PyroBayes On 15 July 2010 19:40, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From chiragmatkarbioinfo at gmail.com Fri Jul 16 11:15:09 2010 From: chiragmatkarbioinfo at gmail.com (chirag matkar) Date: Fri, 16 Jul 2010 20:45:09 +0530 Subject: [Bioperl-l] Perl Web Crawling Message-ID: Hello, My Question Is not based on any Biological Application but in General How can we use Perl extensively in Web Crawling ? -- Regards, Chirag Matkar BTech Bioinformatics From cjfields at illinois.edu Fri Jul 16 11:23:01 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jul 2010 10:23:01 -0500 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <1E0BBB82-C6B4-4351-9133-7E8C4832D252@illinois.edu> http://lmgtfy.com/?q=Perl+Web+crawling chris On Jul 16, 2010, at 10:15 AM, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > > -- > Regards, > Chirag Matkar > BTech Bioinformatics > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From rmb32 at cornell.edu Fri Jul 16 11:23:04 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:04 -0700 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C407958.3010405@cornell.edu> Hi Chirag, This is off-topic for this list, it's not for general Perl questions. Search the CPAN at http://search.cpan.org, there are many modules there that can help you with this. In particular, I would look at WWW::Mechanize. Rob chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From rmb32 at cornell.edu Fri Jul 16 11:23:53 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:53 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: <4C407989.5040609@cornell.edu> My thoughts on this: It sounds like a good plan. Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. So, something to think about going forward. Rob Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From roy.chaudhuri at gmail.com Fri Jul 16 11:24:44 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Fri, 16 Jul 2010 16:24:44 +0100 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C4079BC.5010601@gmail.com> Hi Chirag, This is not an appropriate mailing list for your question, it is intended for discussion of the BioPerl toolkit, not generic bioinformatics or Perl questions. Also, before sending a question to any mailing list you should attempt to answer it yourself. Did you try typing "Perl Web Crawling" into Google? The top few hits look like they may be useful. Cheers, Roy. On 16/07/2010 16:15, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From jun.yin at ucd.ie Fri Jul 16 11:54:36 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Fri, 16 Jul 2010 16:54:36 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign Message-ID: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Dear all, I am the Google Summer of Code student working on refactoring Bio::Align subsystems. The first aim of the project is to recode Bio::SimpleAlign. This is because this package is really useful, but it was created a long time ago, written by several people, and a bit inconsistent mainly due to the above two reasons. I tried to keep the package consistent (e.g. method calling, coding styles) with the previous distribution. However, there are still a few changes. Since this package is created and used by the community, I think it is better to show it to everyone before it is merged with the major distribution. Any suggestions and criticisms are welcome. Here are the major improvements on Bio::SimpleAlign 1. MSA modifying and selection methods are more consistent and easier to use. I have enabled multiple/reverse selections for all sequences/columns selection methods, and change the names to be more understandable. For example, $aln->select() and $aln->select_noncont() are both deprecated, and renamed as $aln->select_Seqs() now. Because selections should be both in seqs and columns, which need to be explicit in the method call. For example, multiple sequence selections can be called by: $newaln=$aln->select_Seqs([4..10,20..35,37]); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37]); Or you can toggle selection(reverse selection) using: $newaln=$aln->select_Seqs([4..10,20..35,37],1); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37],-toggle=>1); If you can the method using the old ways, e.g. $newaln=$aln->select(1,5); A warning will be shown: select - deprecated method. Use select_Seqs() instead. And, the calling will be redirected to $newaln=$aln->select_Seqs([1..5]); 2. gap chars/missing chars are more consistent in the package Default values for gap char and missing char are now set in the package. Calling/Setting gap char should be made by calling $aln->gap_char("-"). 3. Some redundant methods are removed. The methods are moved to more reasonable categories. For example, $aln->select and $aln->select_noncont are deprecated now. Please use $aln->select_Seqs. 4. Some methods are renamed. Methods selecting/giving objects are capitalized, e.g. each_seq to each_Seq. Another example, the method is renamed to give a clearer information. $aln->purge is renamed into $aln->remove_redundant_Seqs $aln->splice_by_seq_pos is renamed to $aln->remove_gaps For further information, you can visit: http://spreadsheets.google.com/ccc?key=0AssLTcJFJMbXdDFfZGpJZlhidFY5blBneGdh QUZ6WFE &hl=en&authkey=CJTCw4QL Cheers, Jun Yin Ph.D. student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin From dan.bolser at gmail.com Fri Jul 16 19:15:03 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 17 Jul 2010 00:15:03 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: On 14 July 2010 11:27, Dan Bolser wrote: > Hi Jason, > > Thanks for the suggestion (see below). > > On 13 July 2010 23:48, Jason Stajich wrote: >> Dan - >> I'm not convinced that contig:example is proper type/source for the >> landmarks & scaffold - i use 'scaffold:chromosome' in my data: >> >> What happens if you change the GFF3 file line from >> ctgA example contig 1 50000 . . . Name=ctgA >> to >> ctgA chromosome scaffold 1 50000 . . . Name=ctgA >> >> >> I think this can be tweaked in the config but there may be different >> defaults for the in memory and DBI::mysql implementation. > > I found that this doesn't make any difference, however, I have found > more information about what causes the bug. > > From my previous email you see that I use bp_seqfeature_load.pl with > the "--namespace volvox" option (I should have guessed it was > something to do with this). Looking closely at the resulting tables I > see that the following tables are empty > > volvox_attribute > volvox_parent2child > volvox_feature > volvox_interval_stats > volvox_name > volvox_parent2child > > > they are not empty when created without the "--namespace x" prefix, > which is why DBI::mysql 'normally' works. > > All the other tables: > > volvox_attributelist > volvox_locationlist > volvox_meta > volvox_sequence > volvox_typelist > > > appear to be created correctly, with or without the "--namespace x" prefix. It might be worth mentioning that this issue can be 'resolved' by not using the -f (fast load) option. i.e. its the specific combination of --namespace and -f that causes the bug. http://bugzilla.open-bio.org/show_bug.cgi?id=3110 > Cheers, > Dan. > >> -jason >> Dan Bolser wrote, On 7/13/10 12:49 AM: >> >> Cheers Chris, >> >> Is there a known good version of >> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? >> I believe that this is one of the more common databases, so I'm >> surprised to find it broken. >> >> What would be the git command to roll back to a stable BioPerl / GBrowse? >> >> >> Sorry for the basic questions, >> Dan. >> >> On 12 July 2010 17:56, Chris Fields wrote: >> >> >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >> >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > From bernd.web at gmail.com Sat Jul 17 08:21:46 2010 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 17 Jul 2010 14:21:46 +0200 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: Dear Jun, Thanks for your work on this. Just a few remarks. -is changing methods names indeed needed? this will break existing code (for some time) -i am not sure how naming is generally done now in BioPerl, but is used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has an "_" followed by a capital. I'd stick with each_seq like names. You now changed it too "each_Seq" but gap_char for example remained gap_char. But surely others know better how/if to change naming. > 2. gap chars/missing chars are more consistent in the package > Default values for gap char and missing char are now set in the package. > Calling/Setting gap char should be made by calling $aln->gap_char("-"). So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char. > Another example, the method is renamed to give a clearer information. > > $aln->purge is renamed into $aln->remove_redundant_Seqs Purge to me is a clear name in aln context ;-) > $aln->splice_by_seq_pos is renamed to $aln->remove_gaps But there was already a remove_gaps method. $aln2 = $aln->remove_gaps Function : Creates an aligment with gaps removed Title : splice_by_seq_pos Usage : $status = splice_by_seq_pos(1); Function: splices all aligned sequences where the specified sequence has gaps. So remove_gaps now takes an optional argument to indicate a 'reference' sequence for splicing? Cheers, Bernd From cjfields at illinois.edu Sat Jul 17 13:07:50 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 12:07:50 -0500 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: On Jul 17, 2010, at 7:21 AM, Bernd Web wrote: > Dear Jun, > > Thanks for your work on this. > Just a few remarks. > -is changing methods names indeed needed? this will break existing > code (for some time) There is expected to be a standard deprecation cycle along with this. Changes would not be merged in until after the 1.6.2 release. > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has > an "_" followed by a capital. I'd stick with each_seq like names. You > now changed it too "each_Seq" but gap_char for example remained > gap_char. But surely others know better how/if to change naming. Technically, we would like to standardize that when object(s) are returned (such as each_seq and it's previous incarnations) the method would have the class in caps, whereas simple data would not. There have been several starts along this path, but I think various methods (next_seq in SeqIO being one) still haven't changed. Also, just to point out, it's not terribly hard to alias these as needed: *eachSeq = \&each_Seq; >> 2. gap chars/missing chars are more consistent in the package >> Default values for gap char and missing char are now set in the package. >> Calling/Setting gap char should be made by calling $aln->gap_char("-"). > So the change here is that now the default values are actually set in > new, instead of setting a the default by calling gap_char. Maybe Jun could answer this, but to me this one makes sense (methods like this, which are relied upon for various reaons, need defaults for proper state). '-' is the most commonly-used symbol. >> Another example, the method is renamed to give a clearer information. >> >> $aln->purge is renamed into $aln->remove_redundant_Seqs > Purge to me is a clear name in aln context ;-) Possibly. However alignments can hold more than sequence data (stockholm format, for example), so maybe purge() on it's own is not descriptive enough. Jun, is remove_redundant_Seqs() an alias/reimplementation for purge()? The name might be a little misleading. >> $aln->splice_by_seq_pos is renamed to $aln->remove_gaps > But there was already a remove_gaps method. > $aln2 = $aln->remove_gaps > Function : Creates an aligment with gaps removed > > Title : splice_by_seq_pos > Usage : $status = splice_by_seq_pos(1); > Function: splices all aligned sequences where the specified sequence > has gaps. > > So remove_gaps now takes an optional argument to indicate a > 'reference' sequence for splicing? > > > Cheers, > Bernd This one I'm not sure about, as the two methods to me seem unrelated from name alone. Jun? chris From cjfields at illinois.edu Sun Jul 18 00:23:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 23:23:49 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <4C407989.5040609@cornell.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> <4C407989.5040609@cornell.edu> Message-ID: On Jul 16, 2010, at 10:23 AM, Robert Buels wrote: > My thoughts on this: > > It sounds like a good plan. > > Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Precisely. > Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. > > If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. > > So, something to think about going forward. > > Rob I mentioned this at BOSC (it's briefly touched upon in the talk); it was agreed that the bottom-up approach is the best. Basically, if we can somehow emulate the larger distribution by allowing installation of the various packages then it makes life much easier for users, just have to decide what is the best approach. chris From rondonbio at yahoo.com.br Sun Jul 18 07:55:44 2010 From: rondonbio at yahoo.com.br (Rondon Neto) Date: Sun, 18 Jul 2010 04:55:44 -0700 (PDT) Subject: [Bioperl-l] Jaccard Dendrogram Message-ID: <750495.60162.qm@web63703.mail.re1.yahoo.com> Hi! Please, can I build a dendrogram from a jaccard distance matrix by Phylogenetic Analysis Pipeline? How to do that? Thank you Rondon From hlapp at drycafe.net Sun Jul 18 10:26:34 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 18 Jul 2010 10:26:34 -0400 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <89E90610-355B-4568-BFE2-301B7F4A7E61@drycafe.net> On Jul 17, 2010, at 8:21 AM, Bernd Web wrote: > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq" each_XXX is the old convention, which we aimed to deprecate before 1.4.x, in fact. Maybe we haven't swept through the entire codebase, but where we can we should certain change it. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From David.Messina at sbc.su.se Sun Jul 18 13:26:52 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 18 Jul 2010 11:26:52 -0600 Subject: [Bioperl-l] Jaccard Dendrogram In-Reply-To: <750495.60162.qm@web63703.mail.re1.yahoo.com> References: <750495.60162.qm@web63703.mail.re1.yahoo.com> Message-ID: Hi Rondon, No, I don't think BioPerl has the ability to do Jaccard distance calculations. Looks like SciPy-cluster can, though: http://code.google.com/p/scipy-cluster/ Also MATLAB probably. However, if you or anyone ese should be so inclined, it should be straightforward to adapt one of the existing BioPerl distance methods. See e.g. Bio::Align::DNAStatistics: http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html Dave On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > Hi! Please, can I build a dendrogram from a jaccard distance matrix by > Phylogenetic Analysis Pipeline? > How to do that? > > Thank you > > Rondon > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From florent.angly at gmail.com Mon Jul 19 04:47:39 2010 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 19 Jul 2010 18:47:39 +1000 Subject: [Bioperl-l] New Bio::Root::IO->_insert() method Message-ID: <4C44112B.1060701@gmail.com> Hi list, I needed a feature to insert text at an arbitrary line in a file for a Bioperl module I am working on. I coded it, called the new method _insert( ) and added it to the Bio::Root::IO module because I realized that it could be useful to other Bioperl modules. The method seems to be working well and does not cause tests to fail but let me know if you encounter issues with it. Regards, Florent From jun.yin at ucd.ie Mon Jul 19 06:43:50 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Mon, 19 Jul 2010 11:43:50 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <004c01cb272f$4626b880$d2742980$%yin@ucd.ie> Hi, Thx for all your comments. 1. About each_seq(each_Seq) As Chris Fields says, we tend to capitalize the method name which returns objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so it is better to use a capitalized name as each_Seq. But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because it may be confused with the each() function in Core. So it may need to be renamed to next_Seq eventually. Usually, what I do for the old method is: sub each_seq { my $self = shift; $self->deprecated("each_seq - deprecated method. Use each_Seq() instead."); $self->each_Seq(); } Thus, if you call the old method, it will still continue to run, but give a deprecated warning. This is done on all deprecated methods. 2. To Bernd Web, " So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char." Yes, gap_char has a default value "-" now, so is missing_char "?" and match_char ".". 3. To Bernd Web and Chris Fields, remove_redundant_Seqs() is just an alias for purge(). However, splice_by_seq_pos() is reimplemented and merged with the old remove_gaps(), because these two methods are actually doing similar things. The new remove_gaps() is: Title : remove_gaps Usage : $aln2 = $aln->remove_gaps(-reference=>5) Function : Creates an aligment with gaps removed Returns : a Bio::SimpleAlign object Args : -GAPCHAR a gap character(optional) if none specified taken from $self->gap_char, -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) indicates that only all-gaps columns should be deleted -REFERENCE splices all aligned sequences where the specified sequence has gaps. If you call the old splice_by_seq_pos(), it will be redirected to remove_gaps() by: sub splice_by_seq_pos{ my $self = shift; $self->deprecated("splice_by_seq_pos - deprecated method. Use remove_gaps() instead."); $self->remove_gaps(-reference=>$_[0]); } When I finally finish the recoding for Bio::SimpleAlign, I will write an online HOWTO. Plus, I think I will include an update log, to show which method is renamed and which is reimplemented, thus to make things clearer. Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin __________ Information from ESET Smart Security, version of virus signature database 5291 (20100719) __________ The message was checked by ESET Smart Security. http://www.eset.com From kellert at ohsu.edu Mon Jul 19 13:05:24 2010 From: kellert at ohsu.edu (Tom Keller) Date: Mon, 19 Jul 2010 10:05:24 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 20 In-Reply-To: References: Message-ID: Greetings, R has a jaccard function also. See http://pbil.univ-lyon1.fr/library/prabclus/html/jaccard.html for a description. cheers, Thomas (Tom) Keller, PhD kellert at ohsu.edu 503.494.2442 6339b R Jones Hall (BSc/CROET) www.ohsu.edu/xd/research/research-cores/dna-analysis/ On Jul 19, 2010, at 9:00 AM, wrote: > Send Bioperl-l mailing list submissions to > bioperl-l at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/bioperl-l > or, via email, send a message with subject or body 'help' to > bioperl-l-request at lists.open-bio.org > > You can reach the person managing the list at > bioperl-l-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioperl-l digest..." > > > Today's Topics: > > 1. Re: Jaccard Dendrogram (Dave Messina) > 2. New Bio::Root::IO->_insert() method (Florent Angly) > 3. Re: Recoding Bio::SimpleAlign (Jun Yin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 18 Jul 2010 11:26:52 -0600 > From: Dave Messina > Subject: Re: [Bioperl-l] Jaccard Dendrogram > To: Rondon Neto > Cc: bioperl-l at lists.open-bio.org > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Hi Rondon, > > No, I don't think BioPerl has the ability to do Jaccard distance > calculations. Looks like SciPy-cluster can, though: > > http://code.google.com/p/scipy-cluster/ > > Also MATLAB probably. > > However, if you or anyone ese should be so inclined, it should be > straightforward to adapt one of the existing BioPerl distance methods. See > e.g. Bio::Align::DNAStatistics: > > http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html > > > > > Dave > > > > > > On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > >> Hi! Please, can I build a dendrogram from a jaccard distance matrix by >> Phylogenetic Analysis Pipeline? >> How to do that? >> >> Thank you >> >> Rondon >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > ------------------------------ > > Message: 2 > Date: Mon, 19 Jul 2010 18:47:39 +1000 > From: Florent Angly > Subject: [Bioperl-l] New Bio::Root::IO->_insert() method > To: bioperl-l BioPerl > Message-ID: <4C44112B.1060701 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi list, > I needed a feature to insert text at an arbitrary line in a file for a > Bioperl module I am working on. I coded it, called the new method > _insert( ) and added it to the Bio::Root::IO module because I realized > that it could be useful to other Bioperl modules. The method seems to be > working well and does not cause tests to fail but let me know if you > encounter issues with it. > Regards, > Florent > > > ------------------------------ > > Message: 3 > Date: Mon, 19 Jul 2010 11:43:50 +0100 > From: Jun Yin > Subject: Re: [Bioperl-l] Recoding Bio::SimpleAlign > To: "'Bernd Web'" > Cc: bioperl-l at lists.open-bio.org, 'Chris Fields' > , bernd.web at gmail.com > Message-ID: <004c01cb272f$4626b880$d2742980$%yin at ucd.ie> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > Thx for all your comments. > > 1. About each_seq(each_Seq) > As Chris Fields says, we tend to capitalize the method name which returns > objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so > it is better to use a capitalized name as each_Seq. > But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because > it may be confused with the each() function in Core. So it may need to be > renamed to next_Seq eventually. > > Usually, what I do for the old method is: > > sub each_seq { > my $self = shift; > $self->deprecated("each_seq - deprecated method. Use each_Seq() > instead."); > $self->each_Seq(); > } > > Thus, if you call the old method, it will still continue to run, but give a > deprecated warning. This is done on all deprecated methods. > > > 2. To Bernd Web, " So the change here is that now the default values are > actually set in new, instead of setting a the default by calling gap_char." > > Yes, gap_char has a default value "-" now, so is missing_char "?" and > match_char ".". > > 3. To Bernd Web and Chris Fields, > remove_redundant_Seqs() is just an alias for purge(). > However, splice_by_seq_pos() is reimplemented and merged with the old > remove_gaps(), because these two methods are actually doing similar things. > The new remove_gaps() is: > > Title : remove_gaps > Usage : $aln2 = $aln->remove_gaps(-reference=>5) > Function : Creates an aligment with gaps removed > Returns : a Bio::SimpleAlign object > Args : -GAPCHAR a gap character(optional) if none specified taken > from $self->gap_char, > -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) > indicates that only all-gaps columns should be deleted > -REFERENCE splices all aligned sequences where the specified > sequence has gaps. > > If you call the old splice_by_seq_pos(), it will be redirected to > remove_gaps() by: > sub splice_by_seq_pos{ > my $self = shift; > $self->deprecated("splice_by_seq_pos - deprecated method. Use > remove_gaps() instead."); > $self->remove_gaps(-reference=>$_[0]); > } > > When I finally finish the recoding for Bio::SimpleAlign, I will write an > online HOWTO. > Plus, I think I will include an update log, to show which method is renamed > and which is reimplemented, thus to make things clearer. > > Cheers, > Jun Yin > Ph.D.?student in U.C.D. > > Bioinformatics Laboratory > Conway Institute > University College Dublin > > > > __________ Information from ESET Smart Security, version of virus signature > database 5291 (20100719) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > > > > > > ------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > End of Bioperl-l Digest, Vol 87, Issue 20 > ***************************************** From jonathan at leto.net Mon Jul 19 18:59:27 2010 From: jonathan at leto.net (Jonathan Leto) Date: Mon, 19 Jul 2010 15:59:27 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: Howdy, I recently found a bug in parsing InterPro XML, which I have created a bug for, as well as patches which fix the problem with a test case: http://bugzilla.open-bio.org/show_bug.cgi?id=3121 I would very much like to get feedback on this patch and have it included in the next 1.6.x release. Thanks, Duke On Thu, Jul 15, 2010 at 9:38 PM, Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. ?This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. ?That will be followed by releases of the run, db, and network distributions. ?Any other thoughts? ?Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jonathan "Duke" Leto jonathan at leto.net http://leto.net From jay at jays.net Mon Jul 19 18:24:05 2010 From: jay at jays.net (Jay Hannah) Date: Mon, 19 Jul 2010 17:24:05 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <9331AD17-C3FB-47E9-80C3-2D1360E9EC8C@jays.net> Greetings, I opened bug 3120 today. Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? http://bugzilla.open-bio.org/show_bug.cgi?id=3120 http://bugzilla.open-bio.org/attachment.cgi?id=1526 Or maybe it's just me? :) Thanks, Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From ycchen1981 at gmail.com Mon Jul 19 23:47:45 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Tue, 20 Jul 2010 11:47:45 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.abi format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my $in = Bio::SeqIO->new(-file => "$inputfilename", -format => 'abi'); my $out = Bio::SeqIO->new(-file => ">$outputfilename", -format => 'phd'); while ( my $seq = $in->next_seq() ) { for my $curr(1 .. $seq->length()) { print "[",$seq->qualat($curr),"]:"; print "[",$seq->trace_index_at($curr),"]\t"; } $out->write_seq($seq); last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From Jonathan_Epstein at nih.gov Tue Jul 20 13:53:00 2010 From: Jonathan_Epstein at nih.gov (Jonathan Epstein) Date: Tue, 20 Jul 2010 13:53:00 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? Message-ID: <4C45E27C.9090400@nih.gov> Hi, I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. Then there's the small matter of loading the hg18 annotations into the appropriate relational database. Thanks in advance for your guidance, Jonathan From rmb32 at cornell.edu Tue Jul 20 14:42:36 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 20 Jul 2010 11:42:36 -0700 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <4C45EE1C.7080401@cornell.edu> Take a look at Bio::DB::SeqFeature::Store. It's got a loader that ships with bioperl, bp_seqfeature_load.pl. perldoc Bio::DB::SeqFeature::Store. From the sound of it, the GMOD/Chado stuff might be too heavyweight for what you are doing. But a good method for accessing a Chado schema from Perl is Bio::Chado::Schema, http://search.cpan.org/perldoc?Bio::Chado::Schema, which is based on DBIx::Class. Hope this helps! Rob Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features > associated with a particular genomic region in the hg18 human assembly. > This seems to require a relational database. Of course I would like to > do this using Bioperl. > > So then the question becomes: what's the best approach to use? > Biosql/BioPerl-db looks like the cleanest solution, but it's not clear > to me how up-to-date it is; it sort of looks like an abandoned project. > > CHADO/Gmod is more actively maintained, but I don't know how/whether I > can obtain BioPerl bindings. > > I am also open to using the UCSC databases as a starting point, since > I've already mirrored most of the human-related portions of the UCSC > environment. > > > Then there's the small matter of loading the hg18 annotations into the > appropriate relational database. > > > Thanks in advance for your guidance, > > Jonathan > > > > > > _______________________________________________ > 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 Jul 20 14:55:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jul 2010 13:55:15 -0500 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <827D02E9-9AA8-4474-BBA4-FC15BAAC49F4@illinois.edu> On Jul 20, 2010, at 12:53 PM, Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. > > So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. Not really abandoned, but it won't help in this case unless you intend on converting to BioSQL. > CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. Look at Bio::Schema:Chado. It's more middleware, no direct BioPerl bindings yet. > I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. > > Then there's the small matter of loading the hg18 annotations into the appropriate relational database. > > Thanks in advance for your guidance, > > Jonathan Bio::DB::SeqFeature::Store. Export the data into GTF; I think the database will load this (via Bio::DB::SeqFeature::Store::GFF2Loader). Otherwise, using the ensembl perl API is an option. One can install the database locally and use the Ensembl Perl API to extract the information you need. There were modules that were intended as interfaces to the remote UCSC databases but (IIRC) there was significant concern from the UCSC folks about overloading the UCSC server with queries, so they were basically deprecated (were only partially developed anyway). chris From hlapp at drycafe.net Tue Jul 20 15:40:10 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 20 Jul 2010 15:40:10 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <0369BC4D-9769-47AE-AF6C-B43BAAEC2327@drycafe.net> On Jul 20, 2010, at 1:53 PM, Jonathan Epstein wrote: > Biosql/BioPerl-db looks like the cleanest solution, but it's not > clear to me how up-to-date it is; it sort of looks like an abandoned > project. It's not abandoned at all. I'm not sure though it serves your use-case - it sounds like some GFF store would meet your needs much better. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From florent.angly at gmail.com Tue Jul 20 18:05:22 2010 From: florent.angly at gmail.com (Florent Angly) Date: Wed, 21 Jul 2010 08:05:22 +1000 Subject: [Bioperl-l] Fwd: gene extraction script Message-ID: <4C461DA2.5090009@gmail.com> -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ From awitney at sgul.ac.uk Wed Jul 21 04:02:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 09:02:01 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <84B8D550-E4CA-4027-99A8-D05F1B5E8DEE@sgul.ac.uk> Hi Nicholas, If you just want to retrieve sequences from GenBank, try this: http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl HTH adam On 20 Jul 2010, at 23:05, Florent Angly wrote: > > > -------- Original Message -------- > Subject: gene extraction script > Date: Tue, 20 Jul 2010 15:56:36 +0100 > From: Nicholas Brown > To: > > > > Hi, > > Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? > Thanks so much for your time in reading this. > > Kind Regards, > > Nicholas Brown > > Script > http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl > #!/usr/bin/perl -w > # $Id$ > =pod > > > =head1 NAME > > > extract_genes.pl - extract genomic sequences from NCBI files > using BioPerl > > > =head1 DESCRIPTION > > > This script is a simple solution to the problem of > extracting genomic regions corresponding to genes. There are other > solutions, this particular approach uses genomic sequence > files from NCBI and gene coordinates from Entrez Gene. > > > The first time this script is run it will be slow as it will > extract species-specific data from the gene2accession file and create > a storable hash (retrieving the positional data from this hash is > significantly faster than reading gene2accession each time the script > runs). The subsequent runs should be fast. > > > =head1 INSTALLATION > > > =head2 > > > Install BioPerl, full instructions at http://bioperl.org. > > > =head2 Download gene2accession.gz > > > Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into > your working directory and gunzip it. > > > =head2 Download sequence files > > > Create one or more species directories in the working directory, the > directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). > > > Download the nucleotide fasta files for a given species from its CHR* > directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a > species directory. The sequence files will have the suffix ".fna" or > "fa.gz", gunzip if necessary. > > > =head2 Determine Taxon id > > > Determine the taxon id for the given species. This id is the first column > in the gene2accession file. Modify the %species hash in this script > such that name of your species directory is a key and the taxon id is the > value. > > > =head2 Command-line options > > > -i Gene id > -s Name of species directory > -h Help > > > Example: > > > extract_genes.pl -i 850302 -s Sc > > > =cut > > > use strict; > use Bio::DB::Fasta; > use Getopt::Long; > use Storable; > > my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae > "Ec" => 83333, # Escherichia coli K12 > "Hs" => 9606 # H. sapiens > ); > > my ($help,$id,$name); > > GetOptions( "s=s" => \$name, > "i=i" => \$id, > "h" => \$help ); > > usage() if ($help || !$id || !$name); > > my $storedHash = $name . ".dump"; > > # create index for a directory of fasta files > my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); > > # extract species-specific data from gene2accession > unless (-e $storedHash) { > my $ref; > # extract species-specific information from gene2accession > open MYIN,"gene2accession" or die "No gene2accession file\n"; > while () { > my @arr = split "\t",$_; > if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { > ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, > $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = > ($arr[9], $arr[10], $arr[11], $arr[7]); > } > } > # save species-specific information using Storable > store $ref, $storedHash; > } > > # retrieve the species-specific data from a stored hash > my $ref = retrieve($storedHash); > > # retrieve sequence and sub-sequence > if (defined $ref->{$id}) { > my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); > my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); > $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); > > # Insert SeqIO options here... > print $seq->seq,"\n"; > } else { > print "Cannot find id: $id\n"; > } > > sub make_my_id { > my $line = shift; > $line =~ /ref\|([^|]+)/; > $1; > } > > sub usage { > system "perldoc $0"; > exit; > } > > __END__ > > > _______________________________________________ > 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 Jul 21 05:43:35 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 10:43:35 +0100 Subject: [Bioperl-l] Fwd: Fwd: gene extraction script References: <4C46B84C.4000702@univ-montp2.fr> Message-ID: forwarding to the original poster and the list... Begin forwarded message: > From: Laurent MANCHON > Date: 21 July 2010 10:05:16 GMT+01:00 > To: Adam Witney > Subject: Re: [Bioperl-l] Fwd: gene extraction script > Reply-To: lmanchon at univ-montp2.fr > > another program you can use. > > > #!/usr/bin/perl > # retrieve sequences from genbank > # read list of GenBank access number from a file and write to output.txt file > > use LWP::UserAgent; > use Bio::SeqIO; > use Bio::DB::GenBank; > $cpt=0; > $outfile = "outfile.txt"; > chomp($outfile); > $gb = new Bio::DB::GenBank; > while (<>) { > ($Fld1) = split(' ', $_, 9999); > $out = Bio::SeqIO->new('-file' => ">>$outfile",'-format' => 'fasta'); > $acc = $Fld1; > $cpt++; > print $acc,"\t$cpt"," retrieved\n"; > $seqio = $gb->get_Stream_by_acc([$acc]); > while( $seq = $seqio->next_seq() ) { > open(LOG,">>$outfile"); > printf LOG '%s ', ">" . $acc; > $out->write_seq($seq); > close(LOG); > } > > > > > > Adam Witney a ?crit : >> >> Hi Nicholas, >> >> If you just want to retrieve sequences from GenBank, try this: >> >> http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl >> >> HTH >> >> adam >> >> >> On 20 Jul 2010, at 23:05, Florent Angly wrote: >> >> >>> -------- Original Message -------- >>> Subject: gene extraction script >>> Date: Tue, 20 Jul 2010 15:56:36 +0100 >>> From: Nicholas Brown >>> To: >>> >>> >>> >>> Hi, >>> >>> Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? >>> Thanks so much for your time in reading this. >>> >>> Kind Regards, >>> >>> Nicholas Brown >>> >>> Script >>> http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl >>> #!/usr/bin/perl -w >>> # $Id$ >>> =pod >>> >>> >>> =head1 NAME >>> >>> >>> extract_genes.pl - extract genomic sequences from NCBI files >>> using BioPerl >>> >>> >>> =head1 DESCRIPTION >>> >>> >>> This script is a simple solution to the problem of >>> extracting genomic regions corresponding to genes. There are other >>> solutions, this particular approach uses genomic sequence >>> files from NCBI and gene coordinates from Entrez Gene. >>> >>> >>> The first time this script is run it will be slow as it will >>> extract species-specific data from the gene2accession file and create >>> a storable hash (retrieving the positional data from this hash is >>> significantly faster than reading gene2accession each time the script >>> runs). The subsequent runs should be fast. >>> >>> >>> =head1 INSTALLATION >>> >>> >>> =head2 >>> >>> >>> Install BioPerl, full instructions at http://bioperl.org. >>> >>> >>> =head2 Download gene2accession.gz >>> >>> >>> Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into >>> your working directory and gunzip it. >>> >>> >>> =head2 Download sequence files >>> >>> >>> Create one or more species directories in the working directory, the >>> directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). >>> >>> >>> Download the nucleotide fasta files for a given species from its CHR* >>> directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a >>> species directory. The sequence files will have the suffix ".fna" or >>> "fa.gz", gunzip if necessary. >>> >>> >>> =head2 Determine Taxon id >>> >>> >>> Determine the taxon id for the given species. This id is the first column >>> in the gene2accession file. Modify the %species hash in this script >>> such that name of your species directory is a key and the taxon id is the >>> value. >>> >>> >>> =head2 Command-line options >>> >>> >>> -i Gene id >>> -s Name of species directory >>> -h Help >>> >>> >>> Example: >>> >>> >>> extract_genes.pl -i 850302 -s Sc >>> >>> >>> =cut >>> >>> >>> use strict; >>> use Bio::DB::Fasta; >>> use Getopt::Long; >>> use Storable; >>> >>> my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae >>> "Ec" => 83333, # Escherichia coli K12 >>> "Hs" => 9606 # H. sapiens >>> ); >>> >>> my ($help,$id,$name); >>> >>> GetOptions( "s=s" => \$name, >>> "i=i" => \$id, >>> "h" => \$help ); >>> >>> usage() if ($help || !$id || !$name); >>> >>> my $storedHash = $name . ".dump"; >>> >>> # create index for a directory of fasta files >>> my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); >>> >>> # extract species-specific data from gene2accession >>> unless (-e $storedHash) { >>> my $ref; >>> # extract species-specific information from gene2accession >>> open MYIN,"gene2accession" or die "No gene2accession file\n"; >>> while () { >>> my @arr = split "\t",$_; >>> if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { >>> ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, >>> $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = >>> ($arr[9], $arr[10], $arr[11], $arr[7]); >>> } >>> } >>> # save species-specific information using Storable >>> store $ref, $storedHash; >>> } >>> >>> # retrieve the species-specific data from a stored hash >>> my $ref = retrieve($storedHash); >>> >>> # retrieve sequence and sub-sequence >>> if (defined $ref->{$id}) { >>> my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); >>> my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); >>> $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); >>> >>> # Insert SeqIO options here... >>> print $seq->seq,"\n"; >>> } else { >>> print "Cannot find id: $id\n"; >>> } >>> >>> sub make_my_id { >>> my $line = shift; >>> $line =~ /ref\|([^|]+)/; >>> $1; >>> } >>> >>> sub usage { >>> system "perldoc $0"; >>> exit; >>> } >>> >>> __END__ >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 jun.yin at ucd.ie Wed Jul 21 06:32:25 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Wed, 21 Jul 2010 11:32:25 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <012201cb28c0$027eb000$077c1000$%yin@ucd.ie> Hi, Nicolas, You don't need to edit the original code. Usually the package developed by the community provides enough methods for you. You may consider to use the recent developed package Bio::DB::EUtilities to retrieve the sequences from GenBank. See HOWTO here: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Florent Angly Sent: Tuesday, July 20, 2010 11:05 PM To: bioperl-l List; n.brown at nhm.ac.uk Subject: [Bioperl-l] Fwd: gene extraction script -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_ge nes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com From amritavisdom at gmail.com Sat Jul 17 07:21:27 2010 From: amritavisdom at gmail.com (AMRITA VISDOM) Date: Sat, 17 Jul 2010 16:51:27 +0530 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita From ycchen1981 at gmail.com Mon Jul 19 03:11:39 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Mon, 19 Jul 2010 15:11:39 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my ?$in ?= Bio::SeqIO->new(-file => "$inputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'abi'); my ?$out = Bio::SeqIO->new(-file => ">$outputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'phd'); while ( my $seq = $in->next_seq() ) { ? ? ? for my $curr(1 .. ?$seq->length()) { ? ? ? ? ? ? ? print "[",$seq->qualat($curr),"]:"; ? ? ? ? ? ? ? print "[",$seq->trace_index_at($curr),"]\t"; ? ? ? } ? ? ? $out->write_seq($seq); ? ? ? last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From amritavisdom at gmail.com Mon Jul 19 07:25:19 2010 From: amritavisdom at gmail.com (Amritavisdom) Date: Mon, 19 Jul 2010 04:25:19 -0700 (PDT) Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: <29203643.post@talk.nabble.com> Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita -- View this message in context: http://old.nabble.com/Parsing-Alternative-Splicing-Gene-information-from-Genbank-file-using-Bioperl-tp29203643p29203643.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From gabriel.jabud at gmail.com Tue Jul 20 14:36:54 2010 From: gabriel.jabud at gmail.com (Gabriel Ab) Date: Tue, 20 Jul 2010 11:36:54 -0700 (PDT) Subject: [Bioperl-l] Finding mutations in Blast files Message-ID: <29216321.post@talk.nabble.com> I'm trying to write a script to find mutations in a Blast output file. The result should look something like [A/G] (query/subject) for SNPs and [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if possible. I was able to get both the query and subject sequence extracted from blast files, but parsing through that for mutations without the help of modules and writing them like above is harder than it sounds. Deletions and other things in the alignment can make it very tricky. I tried looking for modules that would make this task easier but I couldn't find anything. Can someone point me in the right direction on how to do this or let me know about modules that could help? Thanks. -- View this message in context: http://old.nabble.com/Finding-mutations-in-Blast-files-tp29216321p29216321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From taw-bioperl at dowfamily.net Tue Jul 20 19:46:05 2010 From: taw-bioperl at dowfamily.net (Ycart) Date: Tue, 20 Jul 2010 23:46:05 +0000 (UTC) Subject: [Bioperl-l] Accessing karyotype data from Ensembl Message-ID: Hi, I am trying to figure out the correct syntax to access the karyotype data from the Ensembl database. I need to use the start and end base pair coordinates for the karyotype bands in a separate program, which means I need to be able to use that data, not just view it. I'm thinking that it will be like getting slices as described in the Core API Tutorial, but with some other word than 'Slice' in: my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); Any ideas on how to do this under the current API? -Tracy From cjfields at illinois.edu Wed Jul 21 17:43:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 16:43:32 -0500 Subject: [Bioperl-l] Accessing karyotype data from Ensembl In-Reply-To: References: Message-ID: You should contact the ensembl mail list for ensembl-related questions; this lies outside the bioperl domain. chris On Jul 20, 2010, at 6:46 PM, Ycart wrote: > Hi, > > I am trying to figure out the correct syntax to access the karyotype data from > the Ensembl database. I need to use the start and end base pair coordinates for > the karyotype bands in a separate program, which means I need to be able to use > that data, not just view it. > > I'm thinking that it will be like getting slices as described in the Core API > Tutorial, but with some other word than 'Slice' in: > my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); > > > Any ideas on how to do this under the current API? > > > -Tracy > > _______________________________________________ > 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 Jul 21 18:04:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 17:04:48 -0500 Subject: [Bioperl-l] Finding mutations in Blast files In-Reply-To: <29216321.post@talk.nabble.com> References: <29216321.post@talk.nabble.com> Message-ID: <1B5D46EC-BC67-43BB-9376-4A246CB093AD@illinois.edu> On Jul 20, 2010, at 1:36 PM, Gabriel Ab wrote: > > I'm trying to write a script to find mutations in a Blast output file. > The result should look something like [A/G] (query/subject) for SNPs and > [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if > possible. In order to get upstream and downstream you will need access to the original sequence (this information is not reported in the BLAST file). Use the HSP coords to pull that information. > I was able to get both the query and subject sequence extracted from blast > files, but parsing through that for mutations without the help of modules > and writing them like above is harder than it sounds. Deletions and other > things in the alignment can make it very tricky. I tried looking for > modules that would make this task easier but I couldn't find anything. ... > Can someone point me in the right direction on how to do this or let me know > about modules that could help? > > Thanks Bio::Search::HSP::GenericHSP::seq_inds() does something along these lines, e.g. iterates through the two strings by index position and stores relevant information. In this case, you would just print out [X/Y] where there is no match, or [--/XY] when gaps are present. Look at the code for that method to get the general idea. chris From David.Messina at sbc.su.se Wed Jul 21 18:43:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 21 Jul 2010 16:43:07 -0600 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl In-Reply-To: <29203643.post@talk.nabble.com> References: <29203643.post@talk.nabble.com> Message-ID: Hi Amrita, You will want to read the Feature Annotation HOWTO for details of how to parse a Genbank file: http://www.bioperl.org/wiki/HOWTO:Feature-Annotation Dave From cjfields at illinois.edu Wed Jul 21 20:09:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 19:09:05 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: Message-ID: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> It's very possible this is due to API changes within io_lib, but I can't be sure. Aaron, any idea? Just to note, we no longer recommend using the bioperl-ext modules, mainly b/c they have not been actively maintained, so much so that updating them to use the current API is quite difficult (might involve some extensive refactoring). The BioLib project, however, has perl bindings to io_lib. If one had time they could incorporate the BioLib io_lib bindings into bioperl, but I believe ABI support was removed a while ago so that will be problematic. chris On Jul 19, 2010, at 2:11 AM, ??? wrote: > Hi, > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > bioperl-ext-1.5.1, and io-lib-1.8.11; > my OS was 32-bit, Centos 5.2. > When I convert abi-format files to phd-format files, > the value of quality of all bases are '0', and the value of > trace_index of all bases are undefined. > Is there any possible reason leading to this problem? > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > 0.980904.e in phd files; > if this is the case, where can I find phred executers? > > The following is the code utilizing BioPerl and results from BioPerl > and Phred respectively: > ============================================== > #!/usr/bin/perl -w > unshift(@INC, "/opt/BioPerl-1.6.1/"); > unshift(@INC, "/opt/bioperl-ext"); > use strict; > use Bio::SeqIO; > > my $inputfilename='./HMA040184H12.T3.ab1'; > my $outputfilename='test11.phd'; > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > -format => 'abi'); > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > -format => 'phd'); > > while ( my $seq = $in->next_seq() ) { > for my $curr(1 .. $seq->length()) { > print "[",$seq->qualat($curr),"]:"; > print "[",$seq->trace_index_at($curr),"]\t"; > } > $out->write_seq($seq); > last; > } > > ================== test11.phd (by Bio::SeqIO) ================= > BEGIN_SEQUENCE (null) > > BEGIN_COMMENT > > CHROMAT_FILE: unknown > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.980904.e > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Mon Jul 19 11:59:09 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: unknown > CHEM: unknown > DYE: unknown > > END_COMMENT > > BEGIN_DNA > A 0 > G 0 > G 0 > G 0 > G 0 > . > . > . > . > > G 0 > T 0 > T 0 > G 0 > T 0 > C 0 > G 0 > C 0 > T 0 > A 0 > C 0 > END_DNA > > END_SEQUENCE > > ================== .phd (by phred 0.020425.c) ======================= > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > BEGIN_COMMENT > > CHROMAT_FILE: HMA040184H12.T3.ab1 > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.020425.c > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Fri Jul 9 16:20:59 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: 11905 > TRIM: 38 900 0.0500 > TRACE_PEAK_AREA_RATIO: 0.0630 > CHEM: term > DYE: big > > END_COMMENT > > BEGIN_DNA > a 11 2 > g 11 13 > g 11 22 > a 11 37 > a 11 52 > g 8 65 > c 6 76 > t 6 91 > c 6 97 > . > . > . > a 14 11840 > c 16 11849 > a 16 11861 > a 12 11873 > c 12 11885 > g 12 11897 > END_DNA > > END_SEQUENCE > ================================================ > Sincerely yours, > Yen-Chang Chen > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From amackey at virginia.edu Wed Jul 21 20:36:02 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Wed, 21 Jul 2010 20:36:02 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the bioperl-ext modules are not installed? Regardless, can you get a dump of the $seq objects before you hand them off to Bio::SeqIO::phd -- have the qual scores already been lost (problem with the abi reader), or not (problem with the phd writer)? And a basic question -- I assume your .abi files actually have quality values in them (not all do)? -Aaron On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > It's very possible this is due to API changes within io_lib, but I can't be > sure. Aaron, any idea? > > Just to note, we no longer recommend using the bioperl-ext modules, mainly > b/c they have not been actively maintained, so much so that updating them to > use the current API is quite difficult (might involve some extensive > refactoring). The BioLib project, however, has perl bindings to io_lib. If > one had time they could incorporate the BioLib io_lib bindings into bioperl, > but I believe ABI support was removed a while ago so that will be > problematic. > > chris > > On Jul 19, 2010, at 2:11 AM, ??? wrote: > > > Hi, > > > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > > bioperl-ext-1.5.1, and io-lib-1.8.11; > > my OS was 32-bit, Centos 5.2. > > When I convert abi-format files to phd-format files, > > the value of quality of all bases are '0', and the value of > > trace_index of all bases are undefined. > > Is there any possible reason leading to this problem? > > > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > > 0.980904.e in phd files; > > if this is the case, where can I find phred executers? > > > > The following is the code utilizing BioPerl and results from BioPerl > > and Phred respectively: > > ============================================== > > #!/usr/bin/perl -w > > unshift(@INC, "/opt/BioPerl-1.6.1/"); > > unshift(@INC, "/opt/bioperl-ext"); > > use strict; > > use Bio::SeqIO; > > > > my $inputfilename='./HMA040184H12.T3.ab1'; > > my $outputfilename='test11.phd'; > > > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > > -format => 'abi'); > > > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > > -format => 'phd'); > > > > while ( my $seq = $in->next_seq() ) { > > for my $curr(1 .. $seq->length()) { > > print "[",$seq->qualat($curr),"]:"; > > print "[",$seq->trace_index_at($curr),"]\t"; > > } > > $out->write_seq($seq); > > last; > > } > > > > ================== test11.phd (by Bio::SeqIO) ================= > > BEGIN_SEQUENCE (null) > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: unknown > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.980904.e > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Mon Jul 19 11:59:09 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: unknown > > CHEM: unknown > > DYE: unknown > > > > END_COMMENT > > > > BEGIN_DNA > > A 0 > > G 0 > > G 0 > > G 0 > > G 0 > > . > > . > > . > > . > > > > G 0 > > T 0 > > T 0 > > G 0 > > T 0 > > C 0 > > G 0 > > C 0 > > T 0 > > A 0 > > C 0 > > END_DNA > > > > END_SEQUENCE > > > > ================== .phd (by phred 0.020425.c) ======================= > > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: HMA040184H12.T3.ab1 > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.020425.c > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Fri Jul 9 16:20:59 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: 11905 > > TRIM: 38 900 0.0500 > > TRACE_PEAK_AREA_RATIO: 0.0630 > > CHEM: term > > DYE: big > > > > END_COMMENT > > > > BEGIN_DNA > > a 11 2 > > g 11 13 > > g 11 22 > > a 11 37 > > a 11 52 > > g 8 65 > > c 6 76 > > t 6 91 > > c 6 97 > > . > > . > > . > > a 14 11840 > > c 16 11849 > > a 16 11861 > > a 12 11873 > > c 12 11885 > > g 12 11897 > > END_DNA > > > > END_SEQUENCE > > ================================================ > > Sincerely yours, > > Yen-Chang Chen > > > > _______________________________________________ > > 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 Jul 21 22:41:16 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 21:41:16 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Nope; doesn't appear to be a pure-perl parser for this. Was there one? chris On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > bioperl-ext modules are not installed? > > Regardless, can you get a dump of the $seq objects before you hand them off > to Bio::SeqIO::phd -- have the qual scores already been lost (problem with > the abi reader), or not (problem with the phd writer)? > > And a basic question -- I assume your .abi files actually have quality > values in them (not all do)? > > -Aaron > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > >> It's very possible this is due to API changes within io_lib, but I can't be >> sure. Aaron, any idea? >> >> Just to note, we no longer recommend using the bioperl-ext modules, mainly >> b/c they have not been actively maintained, so much so that updating them to >> use the current API is quite difficult (might involve some extensive >> refactoring). The BioLib project, however, has perl bindings to io_lib. If >> one had time they could incorporate the BioLib io_lib bindings into bioperl, >> but I believe ABI support was removed a while ago so that will be >> problematic. >> >> chris >> >> On Jul 19, 2010, at 2:11 AM, ??? wrote: >> >>> Hi, >>> >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, >>> bioperl-ext-1.5.1, and io-lib-1.8.11; >>> my OS was 32-bit, Centos 5.2. >>> When I convert abi-format files to phd-format files, >>> the value of quality of all bases are '0', and the value of >>> trace_index of all bases are undefined. >>> Is there any possible reason leading to this problem? >>> >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is >>> 0.980904.e in phd files; >>> if this is the case, where can I find phred executers? >>> >>> The following is the code utilizing BioPerl and results from BioPerl >>> and Phred respectively: >>> ============================================== >>> #!/usr/bin/perl -w >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); >>> unshift(@INC, "/opt/bioperl-ext"); >>> use strict; >>> use Bio::SeqIO; >>> >>> my $inputfilename='./HMA040184H12.T3.ab1'; >>> my $outputfilename='test11.phd'; >>> >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", >>> -format => 'abi'); >>> >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", >>> -format => 'phd'); >>> >>> while ( my $seq = $in->next_seq() ) { >>> for my $curr(1 .. $seq->length()) { >>> print "[",$seq->qualat($curr),"]:"; >>> print "[",$seq->trace_index_at($curr),"]\t"; >>> } >>> $out->write_seq($seq); >>> last; >>> } >>> >>> ================== test11.phd (by Bio::SeqIO) ================= >>> BEGIN_SEQUENCE (null) >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: unknown >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.980904.e >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Mon Jul 19 11:59:09 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: unknown >>> CHEM: unknown >>> DYE: unknown >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> A 0 >>> G 0 >>> G 0 >>> G 0 >>> G 0 >>> . >>> . >>> . >>> . >>> >>> G 0 >>> T 0 >>> T 0 >>> G 0 >>> T 0 >>> C 0 >>> G 0 >>> C 0 >>> T 0 >>> A 0 >>> C 0 >>> END_DNA >>> >>> END_SEQUENCE >>> >>> ================== .phd (by phred 0.020425.c) ======================= >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: HMA040184H12.T3.ab1 >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.020425.c >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Fri Jul 9 16:20:59 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: 11905 >>> TRIM: 38 900 0.0500 >>> TRACE_PEAK_AREA_RATIO: 0.0630 >>> CHEM: term >>> DYE: big >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> a 11 2 >>> g 11 13 >>> g 11 22 >>> a 11 37 >>> a 11 52 >>> g 8 65 >>> c 6 76 >>> t 6 91 >>> c 6 97 >>> . >>> . >>> . >>> a 14 11840 >>> c 16 11849 >>> a 16 11861 >>> a 12 11873 >>> c 12 11885 >>> g 12 11897 >>> END_DNA >>> >>> END_SEQUENCE >>> ================================================ >>> Sincerely yours, >>> Yen-Chang Chen >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 alperyilmaz at gmail.com Thu Jul 22 00:09:38 2010 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Thu, 22 Jul 2010 00:09:38 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO Message-ID: Hi, I was using Bio::SeqIO with perl one-liner and I noticed an oddity. Can someone suggest a correction or workaround? Let test.fa be; >1 AGTC >2 CTGA Then, commandline below prints the expected output: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < test.fa output: 1 AGTC 2 CTGA However, if use the command in a pipe, then the output has an issue with primary_id of initial sequence. $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' output: AGTC 2 CTGA What is the workaround to make Bio::SeqIO work correctly in a one-liner with pipes? thanks, Alper Yilmaz Post-doctoral Researcher Plant Biotechnology Center The Ohio State University 1060 Carmack Rd Columbus, OH 43210 (614)688-4954 PS: Normally, the example is demonstrating useless use of cat, for the sake giving an example, it can be "command1 | command2 | command3 | perl -MBioSeqIO -e'...' " instead.. From fs5 at sanger.ac.uk Thu Jul 22 06:48:25 2010 From: fs5 at sanger.ac.uk (Frank Schwach) Date: Thu, 22 Jul 2010 11:48:25 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: Message-ID: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Hi Alper, You can actually reproduce it also by providing STDIN from keyboard input like so: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >1 aaaaaaaaa >2 aaaaaaaaa ggggggggg >3 2 ggggggggg ccccccccc 3 ccccccccc In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} then the command returned the sequence of the first entry without the ID again. >From the second entry onwards, it is all correct. I'm not 100% sure but could it be linked to buffering? SeqIO has to read ahead to find a complete entry that spans multiple lines. When you get STDIN from a file, you will get buffering and receive more than one line at once, which will allow the next_seq method to work as expected. If you provide line-by-line input then that method probably can't work correctly. If that is the case then you can't use the command in a pipe at all. Frank On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: > Hi, > > I was using Bio::SeqIO with perl one-liner and I noticed an oddity. > Can someone suggest a correction or workaround? > > Let test.fa be; > >1 > AGTC > >2 > CTGA > > Then, commandline below prints the expected output: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < > test.fa > > output: > 1 AGTC > 2 CTGA > > However, if use the command in a pipe, then the output has an issue > with primary_id of initial sequence. > $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > =>\*STDIN); while ($myseq=$seq->next_seq){ print > $myseq->id,"\t",$myseq->seq,"\n"}' > > output: > AGTC > 2 CTGA > > What is the workaround to make Bio::SeqIO work correctly in a > one-liner with pipes? > > thanks, > > Alper Yilmaz > Post-doctoral Researcher > Plant Biotechnology Center > The Ohio State University > 1060 Carmack Rd > Columbus, OH 43210 > (614)688-4954 > > > PS: Normally, the example is demonstrating useless use of cat, for the > sake giving an example, it can be "command1 | command2 | command3 | > perl -MBioSeqIO -e'...' " instead.. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- 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 roy.chaudhuri at gmail.com Thu Jul 22 07:49:41 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 12:49:41 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Message-ID: <4C483055.5050402@gmail.com> Hi Alper, The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. Cheers. Roy. On 22/07/2010 11:48, Frank Schwach wrote: > Hi Alper, > > You can actually reproduce it also by providing STDIN from keyboard > input like so: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >> 1 > aaaaaaaaa >> 2 > aaaaaaaaa > ggggggggg >> 3 > 2 ggggggggg > ccccccccc > 3 ccccccccc > > In this case I typed > ">1"[ENTER] > "aaaaaaaaa"[ENTER] > ">2"[ENTER} > then the command returned the sequence of the first entry without the ID > again. >> From the second entry onwards, it is all correct. > > I'm not 100% sure but could it be linked to buffering? SeqIO has to read > ahead to find a complete entry that spans multiple lines. When you get > STDIN from a file, you will get buffering and receive more than one line > at once, which will allow the next_seq method to work as expected. If > you provide line-by-line input then that method probably can't work > correctly. > If that is the case then you can't use the command in a pipe at all. > > Frank > > > > On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >> Hi, >> >> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >> Can someone suggest a correction or workaround? >> >> Let test.fa be; >>> 1 >> AGTC >>> 2 >> CTGA >> >> Then, commandline below prints the expected output: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >> test.fa >> >> output: >> 1 AGTC >> 2 CTGA >> >> However, if use the command in a pipe, then the output has an issue >> with primary_id of initial sequence. >> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> $myseq->id,"\t",$myseq->seq,"\n"}' >> >> output: >> AGTC >> 2 CTGA >> >> What is the workaround to make Bio::SeqIO work correctly in a >> one-liner with pipes? >> >> thanks, >> >> Alper Yilmaz >> Post-doctoral Researcher >> Plant Biotechnology Center >> The Ohio State University >> 1060 Carmack Rd >> Columbus, OH 43210 >> (614)688-4954 >> >> >> PS: Normally, the example is demonstrating useless use of cat, for the >> sake giving an example, it can be "command1 | command2 | command3 | >> perl -MBioSeqIO -e'...' " instead.. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From amackey at virginia.edu Thu Jul 22 09:19:52 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 09:19:52 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Message-ID: Hmm, perhaps I'm thinking about the SCF code, not the ABI code. -Aaron On Wed, Jul 21, 2010 at 10:41 PM, Chris Fields wrote: > Nope; doesn't appear to be a pure-perl parser for this. Was there one? > > chris > > On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > > > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > > bioperl-ext modules are not installed? > > > > Regardless, can you get a dump of the $seq objects before you hand them > off > > to Bio::SeqIO::phd -- have the qual scores already been lost (problem > with > > the abi reader), or not (problem with the phd writer)? > > > > And a basic question -- I assume your .abi files actually have quality > > values in them (not all do)? > > > > -Aaron > > > > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields > wrote: > > > >> It's very possible this is due to API changes within io_lib, but I can't > be > >> sure. Aaron, any idea? > >> > >> Just to note, we no longer recommend using the bioperl-ext modules, > mainly > >> b/c they have not been actively maintained, so much so that updating > them to > >> use the current API is quite difficult (might involve some extensive > >> refactoring). The BioLib project, however, has perl bindings to io_lib. > If > >> one had time they could incorporate the BioLib io_lib bindings into > bioperl, > >> but I believe ABI support was removed a while ago so that will be > >> problematic. > >> > >> chris > >> > >> On Jul 19, 2010, at 2:11 AM, ??? wrote: > >> > >>> Hi, > >>> > >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > >>> bioperl-ext-1.5.1, and io-lib-1.8.11; > >>> my OS was 32-bit, Centos 5.2. > >>> When I convert abi-format files to phd-format files, > >>> the value of quality of all bases are '0', and the value of > >>> trace_index of all bases are undefined. > >>> Is there any possible reason leading to this problem? > >>> > >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > >>> 0.980904.e in phd files; > >>> if this is the case, where can I find phred executers? > >>> > >>> The following is the code utilizing BioPerl and results from BioPerl > >>> and Phred respectively: > >>> ============================================== > >>> #!/usr/bin/perl -w > >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); > >>> unshift(@INC, "/opt/bioperl-ext"); > >>> use strict; > >>> use Bio::SeqIO; > >>> > >>> my $inputfilename='./HMA040184H12.T3.ab1'; > >>> my $outputfilename='test11.phd'; > >>> > >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", > >>> -format => 'abi'); > >>> > >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", > >>> -format => 'phd'); > >>> > >>> while ( my $seq = $in->next_seq() ) { > >>> for my $curr(1 .. $seq->length()) { > >>> print "[",$seq->qualat($curr),"]:"; > >>> print "[",$seq->trace_index_at($curr),"]\t"; > >>> } > >>> $out->write_seq($seq); > >>> last; > >>> } > >>> > >>> ================== test11.phd (by Bio::SeqIO) ================= > >>> BEGIN_SEQUENCE (null) > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: unknown > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.980904.e > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Mon Jul 19 11:59:09 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: unknown > >>> CHEM: unknown > >>> DYE: unknown > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> A 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> . > >>> . > >>> . > >>> . > >>> > >>> G 0 > >>> T 0 > >>> T 0 > >>> G 0 > >>> T 0 > >>> C 0 > >>> G 0 > >>> C 0 > >>> T 0 > >>> A 0 > >>> C 0 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> > >>> ================== .phd (by phred 0.020425.c) ======================= > >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: HMA040184H12.T3.ab1 > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.020425.c > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Fri Jul 9 16:20:59 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: 11905 > >>> TRIM: 38 900 0.0500 > >>> TRACE_PEAK_AREA_RATIO: 0.0630 > >>> CHEM: term > >>> DYE: big > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> a 11 2 > >>> g 11 13 > >>> g 11 22 > >>> a 11 37 > >>> a 11 52 > >>> g 8 65 > >>> c 6 76 > >>> t 6 91 > >>> c 6 97 > >>> . > >>> . > >>> . > >>> a 14 11840 > >>> c 16 11849 > >>> a 16 11861 > >>> a 12 11873 > >>> c 12 11885 > >>> g 12 11897 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> ================================================ > >>> Sincerely yours, > >>> Yen-Chang Chen > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/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 Jul 22 09:27:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 08:27:30 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C483055.5050402@gmail.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> Message-ID: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Would someone like to file this as a bug? My guess is this may be a combination of using pipes and the way FASTA is parsed (locally resets $/). http://bugzilla.open-bio.org chris On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > Hi Alper, > > The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. > > Cheers. > Roy. > > On 22/07/2010 11:48, Frank Schwach wrote: >> Hi Alper, >> >> You can actually reproduce it also by providing STDIN from keyboard >> input like so: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >>> 1 >> aaaaaaaaa >>> 2 >> aaaaaaaaa >> ggggggggg >>> 3 >> 2 ggggggggg >> ccccccccc >> 3 ccccccccc >> >> In this case I typed >> ">1"[ENTER] >> "aaaaaaaaa"[ENTER] >> ">2"[ENTER} >> then the command returned the sequence of the first entry without the ID >> again. >>> From the second entry onwards, it is all correct. >> >> I'm not 100% sure but could it be linked to buffering? SeqIO has to read >> ahead to find a complete entry that spans multiple lines. When you get >> STDIN from a file, you will get buffering and receive more than one line >> at once, which will allow the next_seq method to work as expected. If >> you provide line-by-line input then that method probably can't work >> correctly. >> If that is the case then you can't use the command in a pipe at all. >> >> Frank >> >> >> >> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>> Hi, >>> >>> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >>> Can someone suggest a correction or workaround? >>> >>> Let test.fa be; >>>> 1 >>> AGTC >>>> 2 >>> CTGA >>> >>> Then, commandline below prints the expected output: >>> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >>> test.fa >>> >>> output: >>> 1 AGTC >>> 2 CTGA >>> >>> However, if use the command in a pipe, then the output has an issue >>> with primary_id of initial sequence. >>> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>> >>> output: >>> AGTC >>> 2 CTGA >>> >>> What is the workaround to make Bio::SeqIO work correctly in a >>> one-liner with pipes? >>> >>> thanks, >>> >>> Alper Yilmaz >>> Post-doctoral Researcher >>> Plant Biotechnology Center >>> The Ohio State University >>> 1060 Carmack Rd >>> Columbus, OH 43210 >>> (614)688-4954 >>> >>> >>> PS: Normally, the example is demonstrating useless use of cat, for the >>> sake giving an example, it can be "command1 | command2 | command3 | >>> perl -MBioSeqIO -e'...' " instead.. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 roy.chaudhuri at gmail.com Thu Jul 22 09:41:00 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 14:41:00 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C484A6C.1000502@gmail.com> Done (bug 3122). On 22/07/2010 14:27, Chris Fields wrote: > Would someone like to file this as a bug? My guess is this may be a > combination of using pipes and the way FASTA is parsed (locally > resets $/). > > http://bugzilla.open-bio.org > > chris > > On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > >> Hi Alper, >> >> The problem comes about because you don't specify -format=>'fasta' >> in your Bio::SeqIO object. BioPerl attempts to guess the format if >> you don't specify it, but seems to be struggling in this case. I >> can't really think of any good reason for not specifying the >> format. Just in case anyone wants to investigate further, I noticed >> that if you try the example with longer fasta sequences, the first >> line of the sequence is interpreted as the id, with the remainder >> as the sequence. >> >> Cheers. Roy. >> >> On 22/07/2010 11:48, Frank Schwach wrote: >>> Hi Alper, >>> >>> You can actually reproduce it also by providing STDIN from >>> keyboard input like so: $ perl -MBio::SeqIO -e 'my >>> $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> 1 >>> aaaaaaaaa >>>> 2 >>> aaaaaaaaa ggggggggg >>>> 3 >>> 2 ggggggggg ccccccccc 3 ccccccccc >>> >>> In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} >>> then the command returned the sequence of the first entry without >>> the ID again. >>>> From the second entry onwards, it is all correct. >>> >>> I'm not 100% sure but could it be linked to buffering? SeqIO has >>> to read ahead to find a complete entry that spans multiple lines. >>> When you get STDIN from a file, you will get buffering and >>> receive more than one line at once, which will allow the next_seq >>> method to work as expected. If you provide line-by-line input >>> then that method probably can't work correctly. If that is the >>> case then you can't use the command in a pipe at all. >>> >>> Frank >>> >>> >>> >>> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>>> Hi, >>>> >>>> I was using Bio::SeqIO with perl one-liner and I noticed an >>>> oddity. Can someone suggest a correction or workaround? >>>> >>>> Let test.fa be; >>>>> 1 >>>> AGTC >>>>> 2 >>>> CTGA >>>> >>>> Then, commandline below prints the expected output: $ perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}'< test.fa >>>> >>>> output: 1 AGTC 2 CTGA >>>> >>>> However, if use the command in a pipe, then the output has an >>>> issue with primary_id of initial sequence. $ cat test.fa | perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> >>>> output: AGTC 2 CTGA >>>> >>>> What is the workaround to make Bio::SeqIO work correctly in a >>>> one-liner with pipes? >>>> >>>> thanks, >>>> >>>> Alper Yilmaz Post-doctoral Researcher Plant Biotechnology >>>> Center The Ohio State University 1060 Carmack Rd Columbus, OH >>>> 43210 (614)688-4954 >>>> >>>> >>>> PS: Normally, the example is demonstrating useless use of cat, >>>> for the sake giving an example, it can be "command1 | command2 >>>> | command3 | perl -MBioSeqIO -e'...' " instead.. >>>> _______________________________________________ Bioperl-l >>>> mailing list Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 sheetu.piscean at gmail.com Wed Jul 21 17:49:25 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Wed, 21 Jul 2010 14:49:25 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Adding some more details on OS and BioPerl version OS: sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 UTC 2010 i686 GNU/Linux Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi BioPerl Version : sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' 1.006001 Attached is the error that I get while running the RemoteBlast. Thanks, Sheetal On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani wrote: > Hi, > > I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > is the complete script : > #Remote-blast "factory object" creation and blast-parameter > initialization > > use Bio::Tools::Run::RemoteBlast; > use strict; > my $prog = 'blastx'; > my $db = 'nr/nt'; > my $e_val= '1e-10'; > > my @params = ( '-prog' => $prog, > '-data' => $db, > '-expect' => $e_val, > '-readmethod' => 'SearchIO' ); > > my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > #$v is just to turn on and off the messages > my $v = 0; > > my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > ); > > while (my $input = $str->next_seq()){ > #Blast a sequence against a database: > > #Alternatively, you could pass in a file with many > #sequences rather than loop through sequence one at a time > #Remove the loop starting 'while (my $input = $str->next_seq())' > #and swap the two lines below for an example of that. > my $r = $factory->submit_blast($input); > #my $r = $factory->submit_blast('amino.fa'); > > print STDERR "waiting..." if( $v > 0 ); > while ( my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = $factory->retrieve_blast($rid); > if( !ref($rc) ) { > if( $rc < 0 ) { > print "removing rid as rc is < 0"; > $factory->remove_rid($rid); > } > print STDERR "." if ( $v > 0 ); > sleep 5; > } else { > my $result = $rc->next_result(); > #save the output > print "saving to file"; > my $filename = "contig_236.out"; #$result->query_name()."\.out"; > $factory->save_output($filename); > $factory->remove_rid($rid); > print "\nQuery Name: ", $result->query_name(), "\n"; > while ( my $hit = $result->next_hit ) { > next unless ( $v > 0); > print "\thit name is ", $hit->name, "\n"; > while( my $hsp = $hit->next_hsp ) { > print "\t\tscore is ", $hsp->score, "\n"; > } > } > } > } > } > } > > But when I run this, I get an error in html format which says "Cannot > accept request, error code: -103". Attaching the error file for reference. > Can you please help me with debugging this error? Your help is much > appreciated. > > Also, informing about the previous error that I fixed by adding this line: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > I was getting prior to adding this line was : > --------------------- WARNING --------------------- > MSG:

An error has occurred on the > server, The server is unable to format right now, please try again in a few > minutes. If the problem (Informational Message: No alias or index file > found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4CF5MY9101P

> > It kinda took me a while to find out the 2 requirements > > # 1) set your database like this: > -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > > # 2) add this line before submitting the job: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > I think it will be great if you can add this to the synopsis section of > RemoteBlast.pm > > Thanks, > Sheetal > -------------- next part -------------- An HTML attachment was scrubbed... URL: From evelyne.c88 at gmail.com Thu Jul 22 09:57:47 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 06:57:47 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> Message-ID: <29237193.post@talk.nabble.com> Hi, I would like to run a SW alignment, but i'm new to programming... Tried using several tutorials to install this Bioperl-ext package, but not getting that far... Maybe you can help? -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29237193.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From biopython at maubp.freeserve.co.uk Thu Jul 22 10:41:21 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 15:41:21 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29237193.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: > > Hi, > > I would like to run a SW alignment, but i'm new to programming... > Tried using several tutorials to install this Bioperl-ext package, but not > getting that far... > Maybe you can help? How about using the water tool in EMBOSS? I'm sure BioPerl has wrappers for that... http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html Peter From cjfields at illinois.edu Thu Jul 22 11:31:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 10:31:30 -0500 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Jul 22, 2010, at 9:41 AM, Peter wrote: > On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: >> >> Hi, >> >> I would like to run a SW alignment, but i'm new to programming... >> Tried using several tutorials to install this Bioperl-ext package, but not >> getting that far... >> Maybe you can help? > > How about using the water tool in EMBOSS? I'm sure BioPerl has > wrappers for that... > > http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html > > Peter Yes, we do. I would suggest that solution as well; the SW work in bioperl-ext hasn't been maintained actively for a while. That doesn't mean it won't suit your needs, but issues with compilation will likely remained unaddressed. chris From evelyne.c88 at gmail.com Thu Jul 22 10:09:30 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 07:09:30 -0700 (PDT) Subject: [Bioperl-l] installing Bioperl-ext package (Bio::Tools::pSW) Message-ID: <29237314.post@talk.nabble.com> Hi I'm kind of a rookie at programming, but i'm trying to align two sequences. And i would like to use Bio::Tools::pSW I have followed instructions and installed a C compiler (devC++) I read a lot of different tutorials, but cannot find a way to install this package, everything i try gives errors latest error when i tried 'install B/BIRNEY/bioperl-ext-1.4.tar.gz' : c:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site' returned status 512, won't make running make test make had some problems, won't test running make install make had some problems, won't install -- View this message in context: http://old.nabble.com/installing-Bioperl-ext-package-%28Bio%3A%3ATools%3A%3ApSW%29-tp29237314p29237314.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From evelyne.c88 at gmail.com Thu Jul 22 11:21:17 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:21:17 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: <29238161.post@talk.nabble.com> I have really no idea what that means... Studying first year of bio-informatics, and have to make a small perl program as exam Maybe I'm in a bit over my head, I'll ask the tutor for some advice... < References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C4855EE.1010208@bms.com> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm if (defined $self->{-file}) { # Close the file we opened. close($fh); } elsif (ref $fh eq 'GLOB') { # Try seeking to the start position. >>> seek($fh, $start_pos, 0); } elsif (defined $fh && $fh->can('setpos')) { # Seek to the start position. $fh->setpos($start_pos); } return ($done ? $fmt_string : undef); seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset is where the second non-null line starts. I am not sure why- all manuals claim this should work? Hope this helps. Stefan On 7/22/2010 9:27 AM, Chris Fields wrote: > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From biopython at maubp.freeserve.co.uk Thu Jul 22 11:42:25 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 16:42:25 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29238161.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: > > I have really no idea what that means... > Studying first year of bio-informatics, and have to make a small perl > program as exam > Maybe I'm in a bit over my head, I'll ask the tutor for some advice... > The EMBOSS project is a collection of open source command line tools written in C, and includes a tool called "water" for doing Smith Waterman (SW) sequence alignments. I was suggesting you could use BioPerl to call this needle program and parse its output. However, it sounds like you actually have a programming assignment where the point is to actually implement the SW algorithm yourself (in perl). In this case, EMBOSS won't be useful after all. Peter From evelyne.c88 at gmail.com Thu Jul 22 11:53:39 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:53:39 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: <29238557.post@talk.nabble.com> There is actually no real assignment with a goal described. We only have to prove that we understand and can use Perl. (Description of the course states we are to learn the concepts of computer programming, and rudimentary Perl) The Smith Waterman Tool was mentioned during the courses (along with BPlite, and using remote and local BLASTs) so i wanted to explore this, without really knowing how complicated the use of this could be... Maybe they just wanted to let us know what possibilities there are, without expecting that we could do this on our own... Peter-329 wrote: > > On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: >> >> I have really no idea what that means... >> Studying first year of bio-informatics, and have to make a small perl >> program as exam >> Maybe I'm in a bit over my head, I'll ask the tutor for some advice... >> > > The EMBOSS project is a collection of open source command line > tools written in C, and includes a tool called "water" for doing Smith > Waterman (SW) sequence alignments. I was suggesting you could > use BioPerl to call this needle program and parse its output. > > However, it sounds like you actually have a programming assignment > where the point is to actually implement the SW algorithm yourself (in > perl). In this case, EMBOSS won't be useful after all. > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29238557.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From amackey at virginia.edu Thu Jul 22 13:15:18 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 13:15:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C4855EE.1010208@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. -Aaron On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov wrote: > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset > is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> > > > _______________________________________________ > 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 Jul 22 14:35:51 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 13:35:51 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C48853F.3050904@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): tell() on pipes, fifos, and sockets usually returns -1. My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: if (!$self->seekable) { #die a horrible death } chris On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). > I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) > I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. > Another option is to right to a temp file or slurp into memory. This could be dangerous though... > > On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >> >> -Aaron >> >> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: >> >> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >> >> if (defined $self->{-file}) { >> # Close the file we opened. >> close($fh); >> } elsif (ref $fh eq 'GLOB') { >> # Try seeking to the start position. >> >>> seek($fh, $start_pos, 0); >> } elsif (defined $fh && $fh->can('setpos')) { >> # Seek to the start position. >> $fh->setpos($start_pos); >> } >> return ($done ? $fmt_string : undef); >> >> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >> after reset is where the second non-null line starts. >> I am not sure why- all manuals claim this should work? >> Hope this helps. >> Stefan >> >> On 7/22/2010 9:27 AM, Chris Fields wrote: >> >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > From dunlopjp.ctr at afrl.hpc.mil Thu Jul 22 12:35:01 2010 From: dunlopjp.ctr at afrl.hpc.mil (Mr. James P. Dunlop (Contractor)) Date: Thu, 22 Jul 2010 12:35:01 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org Message-ID: <4C487335.4080808@afrl.hpc.mil> Hello I very new to this type of install. I am trying to install this as non root, which may be part of the problem, but I thought I found some information that addresses this. Also I'm trying to use cpan. The error before termination is: Files=44, Tests=1140, 30 wallclock secs (22.97 cusr + 6.94 csys = 29.91 CPU) /usr/bin/make test -- OK Running make install /usr/bin/perl Build --makefile_env_macros 1 install Building Module-Build Writing /app/bioperl/BioPerl-1.6.0/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Module/Build/.packlist /usr/bin/make install -- OK Couldn't install Module::Build, giving up. Running make test Make had some problems, maybe interrupted? Won't test Running make install Make had some problems, maybe interrupted? Won't install cpan> Is there anything that is obvious to you folks? Would it be possible to cc any e-mails to dunlopjp at aol.com? Thanks Jim Dunlop 937-255-0050 From stefan.kirov at bms.com Thu Jul 22 13:51:59 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 13:51:59 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: <4C48853F.3050904@bms.com> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. Another option is to right to a temp file or slurp into memory. This could be dangerous though... On 7/22/2010 1:15 PM, Aaron Mackey wrote: > You cannot seek on a pipe, unfortunately. SeqIO should probably try > to detect this, and die rather than invoking GuessSeqFormat. > > -Aaron > > On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: > > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh > after reset is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From stefan.kirov at bms.com Thu Jul 22 15:37:18 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 15:37:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: <4C489DEE.1010806@bms.com> Chris, I tested tell and for me it actually returns the correct position. I think seek($fh, $start_pos, 0) || $self->throw("Failed resetting the filehandle pointer; IO error occurred"); might be better. On 7/22/2010 2:35 PM, Chris Fields wrote: > It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): > > tell() on pipes, fifos, and sockets usually returns -1. > > My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: > > if (!$self->seekable) { > #die a horrible death > } > > chris > > On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > > >> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). >> I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) >> I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. >> Another option is to right to a temp file or slurp into memory. This could be dangerous though... >> >> On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> >>> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >>> >>> -Aaron >>> >>> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov> wrote: >>> >>> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >>> >>> if (defined $self->{-file}) { >>> # Close the file we opened. >>> close($fh); >>> } elsif (ref $fh eq 'GLOB') { >>> # Try seeking to the start position. >>> >>> seek($fh, $start_pos, 0); >>> } elsif (defined $fh&& $fh->can('setpos')) { >>> # Seek to the start position. >>> $fh->setpos($start_pos); >>> } >>> return ($done ? $fmt_string : undef); >>> >>> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >>> after reset is where the second non-null line starts. >>> I am not sure why- all manuals claim this should work? >>> Hope this helps. >>> Stefan >>> >>> On 7/22/2010 9:27 AM, Chris Fields wrote: >>> >>> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> >>> $myseq->id,"\t",$myseq->seq,"\n"} >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >> >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From cjfields at illinois.edu Thu Jul 22 19:54:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 18:54:20 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? chris On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > Adding some more details on OS and BioPerl version > > OS: > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > UTC 2010 i686 GNU/Linux > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > BioPerl Version : > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > 'print $Bio::Root::Version::VERSION,"\n"' > 1.006001 > > Attached is the error that I get while running the RemoteBlast. > > Thanks, > Sheetal > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > wrote: > >> Hi, >> >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here >> is the complete script : >> #Remote-blast "factory object" creation and blast-parameter >> initialization >> >> use Bio::Tools::Run::RemoteBlast; >> use strict; >> my $prog = 'blastx'; >> my $db = 'nr/nt'; >> my $e_val= '1e-10'; >> >> my @params = ( '-prog' => $prog, >> '-data' => $db, >> '-expect' => $e_val, >> '-readmethod' => 'SearchIO' ); >> >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); >> >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; >> >> #$v is just to turn on and off the messages >> my $v = 0; >> >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' >> ); >> >> while (my $input = $str->next_seq()){ >> #Blast a sequence against a database: >> >> #Alternatively, you could pass in a file with many >> #sequences rather than loop through sequence one at a time >> #Remove the loop starting 'while (my $input = $str->next_seq())' >> #and swap the two lines below for an example of that. >> my $r = $factory->submit_blast($input); >> #my $r = $factory->submit_blast('amino.fa'); >> >> print STDERR "waiting..." if( $v > 0 ); >> while ( my @rids = $factory->each_rid ) { >> foreach my $rid ( @rids ) { >> my $rc = $factory->retrieve_blast($rid); >> if( !ref($rc) ) { >> if( $rc < 0 ) { >> print "removing rid as rc is < 0"; >> $factory->remove_rid($rid); >> } >> print STDERR "." if ( $v > 0 ); >> sleep 5; >> } else { >> my $result = $rc->next_result(); >> #save the output >> print "saving to file"; >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; >> $factory->save_output($filename); >> $factory->remove_rid($rid); >> print "\nQuery Name: ", $result->query_name(), "\n"; >> while ( my $hit = $result->next_hit ) { >> next unless ( $v > 0); >> print "\thit name is ", $hit->name, "\n"; >> while( my $hsp = $hit->next_hsp ) { >> print "\t\tscore is ", $hsp->score, "\n"; >> } >> } >> } >> } >> } >> } >> >> But when I run this, I get an error in html format which says "Cannot >> accept request, error code: -103". Attaching the error file for reference. >> Can you please help me with debugging this error? Your help is much >> appreciated. >> >> Also, informing about the previous error that I fixed by adding this line: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that >> I was getting prior to adding this line was : >> --------------------- WARNING --------------------- >> MSG:

An error has occurred on the >> server, The server is unable to format right now, please try again in a few >> minutes. If the problem (Informational Message: No alias or index file >> found for protein database [nr/nt] in search path >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: >> 4CF5MY9101P

>> >> It kinda took me a while to find out the 2 requirements >> >> # 1) set your database like this: >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options >> >> >> # 2) add this line before submitting the job: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; >> >> I think it will be great if you can add this to the synopsis section of >> RemoteBlast.pm >> >> Thanks, >> Sheetal >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Thu Jul 22 19:52:19 2010 From: genehack at genehack.org (John Anderson) Date: Thu, 22 Jul 2010 19:52:19 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: <4C487335.4080808@afrl.hpc.mil> References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: The one thing that sticks out is this: > Couldn't install Module::Build, giving up. Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. chrs, john. From cjfields at illinois.edu Thu Jul 22 21:53:36 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:53:36 -0500 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 6:52 PM, John Anderson wrote: > > On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: > > The one thing that sticks out is this: > >> Couldn't install Module::Build, giving up. > > Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. > > chrs, > john. Also helps to set any CPAN configuration to install locally. http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA chris From cjfields at illinois.edu Thu Jul 22 21:52:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:52:15 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Removing this line from your original script worked for me: $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; This is set via '-prog' parameter. chris On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". > > Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : > An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > Adding below the email conversation with blast-help for debugging further : > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: > Sheetal, > > You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. > > Best regards, > Wayne > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. > > The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. > > Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. > > Thanks, > Sheetal > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: > Hello, > > Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > Best regards, > Wayne > > _~___~___~__~__~_~ > Wayne Matten, PhD > NCBI Public Services > mattenw at mail.nih.gov > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > Hello, > > I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : > Cannot accept request, error code: -103 > > The request that I send is : > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx >> >> Can you please help me debug it. >> >> Thanks and Regards, >> Sheetal > > Thanks > Sheetal > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sheetu.piscean at gmail.com Thu Jul 22 20:30:24 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Thu, 22 Jul 2010 17:30:24 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. Adding below the email conversation with blast-help for debugging further : On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: Sheetal, You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. Best regards, Wayne http://www.ncbi.nlm.nih.gov/blast /Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. Thanks, Sheetal On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: Hello, Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo Best regards, Wayne _~___~___~__~__~_~ Wayne Matten, PhD NCBI Public Services mattenw at mail.nih.gov On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: Hello, I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : Cannot accept request, error code: -103 The request that I send is : POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx Can you please help me debug it. Thanks and Regards, Sheetal Thanks Sheetal On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version > -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for > reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this > line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a > few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From shachigahoimbi at gmail.com Fri Jul 23 07:01:01 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:31:01 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From shachigahoimbi at gmail.com Fri Jul 23 07:28:05 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:58:05 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From giles.weaver at bbsrc.ac.uk Fri Jul 23 07:31:11 2010 From: giles.weaver at bbsrc.ac.uk (Giles Weaver) Date: Fri, 23 Jul 2010 12:31:11 +0100 Subject: [Bioperl-l] bioperl modules In-Reply-To: References: Message-ID: <4C497D7F.1060806@bbsrc.ac.uk> See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. Regards, Giles On 23/07/10 12:01, Shachi Gahoi wrote: > I want to use following bioperl modules. I have installed bioperl 1.6.I. > have searched all modules in it but i have not found following modules. I > want to use it. please tell me if anyone know about these modules and use of > it. > > temp- for temperature checking > ac- for count of AC content > gc- for count of GC content > dimer- check bases for dimerization > check 5- Check the presence of GC, CG, C or G at 5' > check 3- Check the presence of GC, CG, C or G at 3' > basepair- calculate % of GC > hairpin- calculate hairpin structure > delta- calculate delta G value for primer > temp diff- check for temperature difference in left and right primer > > please tell me if anyone know about these modules. > > Thanks in advance > > > From cjfields at illinois.edu Fri Jul 23 09:17:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 08:17:41 -0500 Subject: [Bioperl-l] bioperl modules In-Reply-To: <4C497D7F.1060806@bbsrc.ac.uk> References: <4C497D7F.1060806@bbsrc.ac.uk> Message-ID: <688164AF-AF7B-49D0-9E68-A4916C7A2DDC@illinois.edu> This sounds suspiciously like homework, so I'm reluctant to give any direct answers. Most (all?) of these are covered in the Tisdall books, IIRC, and all use regexes or transliteration, that's about all I'll say. chris On Jul 23, 2010, at 6:31 AM, Giles Weaver wrote: > See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. > Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. > > Regards, > > Giles > > On 23/07/10 12:01, Shachi Gahoi wrote: >> I want to use following bioperl modules. I have installed bioperl 1.6.I. >> have searched all modules in it but i have not found following modules. I >> want to use it. please tell me if anyone know about these modules and use of >> it. >> >> temp- for temperature checking >> ac- for count of AC content >> gc- for count of GC content >> dimer- check bases for dimerization >> check 5- Check the presence of GC, CG, C or G at 5' >> check 3- Check the presence of GC, CG, C or G at 3' >> basepair- calculate % of GC >> hairpin- calculate hairpin structure >> delta- calculate delta G value for primer >> temp diff- check for temperature difference in left and right primer >> >> please tell me if anyone know about these modules. >> >> Thanks in advance >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From pg4 at sanger.ac.uk Fri Jul 23 04:06:38 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 09:06:38 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' Message-ID: Hello, Regarding the recent post about installing bioperl as non root, http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique http://perl.jonallen.info/writing/articles/install-perl-modules-without-root I wanted to put it in the talk page first, but there is an 'issue': The talk link points to http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix Talk:Installing Bioperl for Unix 2 and in this talk page, the page link point to a deleted page http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 Editing Installing Bioperl for Unix 2 Warning: You are recreating a page that was previously deleted. You should consider whether it is appropriate to continue editing this page. The deletion log for this page is provided here for convenience: * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing Bioperl for Unix 2" ? (testing out page (adding back from file)) Just to let you know. ----- Pablo Marin-Garcia -- 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 Fri Jul 23 11:07:23 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 10:07:23 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: Message-ID: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Pablo, No idea how that happened, but I removed the older discussion page and my obsolete comment, along with the redirect on the main discussion page. Edit away! chris On Jul 23, 2010, at 3:06 AM, Pablo Marin-Garcia wrote: > Hello, > > Regarding the recent post about installing bioperl as non root, > > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. > > http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique > http://perl.jonallen.info/writing/articles/install-perl-modules-without-root > > I wanted to put it in the talk page first, but there is an 'issue': > > The talk link points to > http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix > Talk:Installing Bioperl for Unix 2 > > and in this talk page, the page link point to a deleted page > http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 > > Editing Installing Bioperl for Unix 2 > Warning: You are recreating a page that was previously deleted. > > You should consider whether it is appropriate to continue editing this page. > The deletion log for this page is provided here for convenience: > > * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing > Bioperl > for Unix 2" ? (testing out page (adding back from file)) > > > Just to let you know. > > ----- > > Pablo Marin-Garcia > > > > -- > 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. > _______________________________________________ > 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 Fri Jul 23 11:42:09 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 09:42:09 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: Thanks for that addition to the wiki, Pablo! Much appreciated. I did not know about local::lib. Dave From pg4 at sanger.ac.uk Fri Jul 23 12:52:03 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 17:52:03 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Dave Messina wrote: > Thanks for that addition to the wiki, Pablo! Much appreciated. > > I did not know about local::lib. > [This is a bit off-topic but probably useful for core developers] Then probably you don't know about App::perlbrew Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ---- Copied from the SYNOPSIS: # Initialize perlbrew init # Install some Perls perlbrew install perl-5.8.1 perlbrew install perl-5.11.5 # See what were installed perlbrew installed # Switch perl in the $PATH perlbrew switch perl-5.11.5 perl -v # Switch to another version perlbrew switch perl-5.8.1 perl -v # Switch to a certain perl executable not managed by perlbrew. perlbrew switch /usr/bin/perl # Or turn it off completely. Useful when you messed up too deep. perlbrew off # Use 'switch' command to turn it back on. perlbrew switch perl-5.11.5 -Pablo > > Dave > ----- Pablo Marin-Garcia -- 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 Fri Jul 23 12:57:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 11:57:05 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ... yes, just started using this myself. Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. chris From cjfields at illinois.edu Fri Jul 23 13:01:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:01:20 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ...and completely forgot to mention the tremendous benefits of App::perlbrew for development! Lots of very nice tools becoming available these days... chris From cjfields at illinois.edu Fri Jul 23 13:20:44 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:20:44 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> http://github.com/cjfields/bioperl6 http://github.com/cjfields/biome :) chris On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > > extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: > > http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html > > I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. > > > Have a good weekend > > -Pablo > > > > On Fri, 23 Jul 2010, Chris Fields wrote: > >> >> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >> >>> On Fri, 23 Jul 2010, Dave Messina wrote: >>> >>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>> >>>> I did not know about local::lib. >>>> >>> >>> [This is a bit off-topic but probably useful for core developers] >>> Then probably you don't know about >>> >>> App::perlbrew >>> >>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >> ... >> >> yes, just started using this myself. >> >> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >> >> chris > > > ----- > > Pablo Marin-Garcia > > > > -- > 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 sheetu.piscean at gmail.com Fri Jul 23 13:04:59 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 10:04:59 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: I did remove that line but doesn't help. I still keep getting this error: MSG:

An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4KJE1YJ601N

Any pointers ?? - Sheetal On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > This is set via '-prog' parameter. > > chris > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to Blast-help as well > and they have to say that "there is something wrong with the URL, didn't > give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default it is set to > plain, I guess this value is for standard blast pgm. like blastp, blastx, > etc) gives me this error : > > An error has occurred on the server, The server is unable to format right > now, please try again in a few minutes. If the problem (Informational > Message: No alias or index file found for protein database [nr/nt] in search > path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for debugging further > : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some errors. The > URL below works; note that order of parameters does not matter. > > > > Best regards, > > Wayne > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning immediately after > "QUERY=", (called as bare sequence) but still I get the same error. > > > > The documentation on your URLAPI says that Query can have Accession(s), > gi(S) or FASTA sequence. The format of the query for FASTA sequence is as > shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA > sequence, the query has description/definition followed by actual sequence. > In that case, the format of my POST request match the requirement. > > > > Can you help me figure out why am I still getting error : "Cannot accept > request, error code: -103" ? Attaching the log file having Query as bare > sequence and FASTA sequence for your reference. Your help is much > appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not use, requires > that the sequence begin immediately after "QUERY=". Your example shows a > definition line preceding the sequence. You can get documentation on our > URLAPI on this page (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my Bioperl script > remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded > DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 > 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a time > > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; > #$result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which says "Cannot > > >> accept request, error code: -103". Attaching the error file for > reference. > > >> Can you please help me with debugging this error? Your help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by adding this > line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has occurred on > the > > >> server, The server is unable to format right now, please try again in > a few > > >> minutes. If the problem (Informational Message: No alias or index > file > > >> found for protein database [nr/nt] in search path > > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the synopsis section > of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > From pg4 at sanger.ac.uk Fri Jul 23 13:17:50 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:17:50 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. Have a good weekend -Pablo On Fri, 23 Jul 2010, Chris Fields wrote: > > On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > >> On Fri, 23 Jul 2010, Dave Messina wrote: >> >>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>> >>> I did not know about local::lib. >>> >> >> [This is a bit off-topic but probably useful for core developers] >> Then probably you don't know about >> >> App::perlbrew >> >> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. > ... > > yes, just started using this myself. > > Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. > > chris ----- Pablo Marin-Garcia -- 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 Fri Jul 23 13:36:40 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:36:40 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> I've attached the code and example data that worked. This is using the latest bioperl on github, so maybe it's the version you have installed? chris On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > I did remove that line but doesn't help. I still keep getting this > error: > MSG:

An error has occurred on > the server, The server is unable to format right now, please try again > in a few minutes. If the problem (Informational Message: No alias or > index file found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4KJE1YJ601N

> > Any pointers ?? > > - Sheetal > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > This is set via '-prog' parameter. > > chris > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to > Blast-help as well and they have to say that "there is > something wrong with the URL, didn't give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default > it is set to plain, I guess this value is for standard blast > pgm. like blastp, blastx, etc) gives me this error : > > An error has occurred on the server, The server is unable to > format right now, please try again in a few minutes. If the > problem (Informational Message: No alias or index file found > for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for > debugging further : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some > errors. The URL below works; note that order of parameters > does not matter. > > > > Best regards, > > Wayne > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > 3EContig_236+%0A% > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning > immediately after "QUERY=", (called as bare sequence) but > still I get the same error. > > > > The documentation on your URLAPI says that Query can have > Accession(s), gi(S) or FASTA sequence. The format of the query > for FASTA sequence is as shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > for FASTA sequence, the query has description/definition > followed by actual sequence. In that case, the format of my > POST request match the requirement. > > > > Can you help me figure out why am I still getting error : > "Cannot accept request, error code: -103" ? Attaching the log > file having Query as bare sequence and FASTA sequence for your > reference. Your help is much appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not > use, requires that the sequence begin immediately after > "QUERY=". Your example shows a definition line preceding the > sequence. You can get documentation on our URLAPI on this page > (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my > Bioperl script remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > 3EContig_236+% > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI > server, not problems with the script. Is this still > occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > Jun 11 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the > RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on > 'nr' database. Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and > blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > -format => 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a > time > > >> #Remove the loop starting 'while (my $input = > $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; # > $result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), > "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which > says "Cannot > > >> accept request, error code: -103". Attaching the error > file for reference. > > >> Can you please help me with debugging this error? Your > help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by > adding this line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; The error that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has > occurred on the > > >> server, The server is unable to format right now, please > try again in a few > > >> minutes. If the problem (Informational Message: No > alias or index file > > >> found for protein database [nr/nt] in search path > > >> > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 > requirements > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the > synopsis section of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: test.pl Type: application/x-perl Size: 2211 bytes Desc: not available URL: -------------- next part -------------- >Foo My description here AATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGG CGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGA GGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCT CCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCC ACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAG AAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCAT GGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAAT GCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCC TGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCG GGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGA TTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGC CCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAG CCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAAT CCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGG CTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTAT ACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCT CAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGC GCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACG CAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTG TCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTC AGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGAT GAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTG CGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCAC GCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGA GACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACT CAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCA TCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAAC AGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAG CGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTT CTGT From pg4 at sanger.ac.uk Fri Jul 23 13:33:10 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:33:10 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Chris Fields wrote: > http://github.com/cjfields/bioperl6 oh, very nice!. > http://github.com/cjfields/biome one of my to-do things for my holidays is to git clone it and star to play with it. I have several mOOse modules for GWAS that I am going to release soon but I would like to accomodate them first to the bioperl look and feel. > :) > > chris > > On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > >> >> extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: >> >> http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html >> >> I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. >> >> >> Have a good weekend >> >> -Pablo >> >> >> >> On Fri, 23 Jul 2010, Chris Fields wrote: >> >>> >>> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >>> >>>> On Fri, 23 Jul 2010, Dave Messina wrote: >>>> >>>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>>> >>>>> I did not know about local::lib. >>>>> >>>> >>>> [This is a bit off-topic but probably useful for core developers] >>>> Then probably you don't know about >>>> >>>> App::perlbrew >>>> >>>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >>> ... >>> >>> yes, just started using this myself. >>> >>> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >>> >>> chris >> >> >> ----- >> >> Pablo Marin-Garcia >> >> >> >> -- >> 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. > > ----- Pablo Marin-Garcia -- 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 sheetu.piscean at gmail.com Fri Jul 23 14:15:51 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 11:15:51 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> References: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> Message-ID: Thanks a lot Chris. It worked for me as well :) - Sheetal On Fri, Jul 23, 2010 at 10:36 AM, Chris Fields wrote: > I've attached the code and example data that worked. This is using the > latest bioperl on github, so maybe it's the version you have installed? > > chris > > On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > > I did remove that line but doesn't help. I still keep getting this > > error: > > MSG:

An error has occurred on > > the server, The server is unable to format right now, please try again > > in a few minutes. If the problem (Informational Message: No alias or > > index file found for protein database [nr/nt] in search path > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > 4KJE1YJ601N

> > > > Any pointers ?? > > > > - Sheetal > > > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > > wrote: > > Removing this line from your original script worked for me: > > > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > > > > This is set via '-prog' parameter. > > > > chris > > > > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > > > Yes the error is still occurring. I have emailed to > > Blast-help as well and they have to say that "there is > > something wrong with the URL, didn't give any specifics". > > > > > > Also changing the parameter SERVICE to 'plain' (by default > > it is set to plain, I guess this value is for standard blast > > pgm. like blastp, blastx, etc) gives me this error : > > > An error has occurred on the server, The server is unable to > > format right now, please try again in a few minutes. If the > > problem (Informational Message: No alias or index file found > > for protein database [nr/nt] in search path > > > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I > have sent an email today to blast-help for this error. > > > > > > Adding below the email conversation with blast-help for > > debugging further : > > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > > wrote: > > > Sheetal, > > > > > > You are right about the query syntax, but your URL has some > > errors. The URL below works; note that order of parameters > > does not matter. > > > > > > Best regards, > > > Wayne > > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > > 3EContig_236+%0A% > > > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > > > Thank you Wayne. I tried with the sequence beginning > > immediately after "QUERY=", (called as bare sequence) but > > still I get the same error. > > > > > > The documentation on your URLAPI says that Query can have > > Accession(s), gi(S) or FASTA sequence. The format of the query > > for FASTA sequence is as shown: > > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > > for FASTA sequence, the query has description/definition > > followed by actual sequence. In that case, the format of my > > POST request match the requirement. > > > > > > Can you help me figure out why am I still getting error : > > "Cannot accept request, error code: -103" ? Attaching the log > > file having Query as bare sequence and FASTA sequence for your > > reference. Your help is much appreciated. > > > > > > Thanks, > > > Sheetal > > > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > > wrote: > > > Hello, > > > > > > Our URLAPI, which your script should, but may or may not > > use, requires that the sequence begin immediately after > > "QUERY=". Your example shows a definition line preceding the > > sequence. You can get documentation on our URLAPI on this page > > (Web service interface): > > > > > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > > > Best regards, > > > Wayne > > > > > > _~___~___~__~__~_~ > > > Wayne Matten, PhD > > > NCBI Public Services > > > mattenw at mail.nih.gov > > > > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > Hello, > > > > > > I am trying to use blastx program with 'nr' database in my > > Bioperl script remotely. While I do so, I get this error : > > > Cannot accept request, error code: -103 > > > > > > The request that I send is : > > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > > bioperl-Bio_Tools_Run_ > > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > > 3EContig_236+% > > > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > > >> > > >> Can you please help me debug it. > > >> > > >> Thanks and Regards, > > >> Sheetal > > > > > > Thanks > > > Sheetal > > > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > > wrote: > > > The errors reported seem to indicate problems on the NCBI > > server, not problems with the script. Is this still > > occurring? > > > > > > chris > > > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > > Adding some more details on OS and BioPerl version > > > > > > > > OS: > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > > Jun 11 07:54:58 > > > > UTC 2010 i686 GNU/Linux > > > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > > > BioPerl Version : > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > > -MBio::Root::Version -e > > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > > 1.006001 > > > > > > > > Attached is the error that I get while running the > > RemoteBlast. > > > > > > > > Thanks, > > > > Sheetal > > > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > > wrote: > > > > > > > >> Hi, > > > >> > > > >> I am trying to run RemoteBlast to blastx sequences on > > 'nr' database. Here > > > >> is the complete script : > > > >> #Remote-blast "factory object" creation and > > blast-parameter > > > >> initialization > > > >> > > > >> use Bio::Tools::Run::RemoteBlast; > > > >> use strict; > > > >> my $prog = 'blastx'; > > > >> my $db = 'nr/nt'; > > > >> my $e_val= '1e-10'; > > > >> > > > >> my @params = ( '-prog' => $prog, > > > >> '-data' => $db, > > > >> '-expect' => $e_val, > > > >> '-readmethod' => 'SearchIO' ); > > > >> > > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > > >> > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; > > > >> > > > >> #$v is just to turn on and off the messages > > > >> my $v = 0; > > > >> > > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > > -format => 'fasta' > > > >> ); > > > >> > > > >> while (my $input = $str->next_seq()){ > > > >> #Blast a sequence against a database: > > > >> > > > >> #Alternatively, you could pass in a file with many > > > >> #sequences rather than loop through sequence one at a > > time > > > >> #Remove the loop starting 'while (my $input = > > $str->next_seq())' > > > >> #and swap the two lines below for an example of that. > > > >> my $r = $factory->submit_blast($input); > > > >> #my $r = $factory->submit_blast('amino.fa'); > > > >> > > > >> print STDERR "waiting..." if( $v > 0 ); > > > >> while ( my @rids = $factory->each_rid ) { > > > >> foreach my $rid ( @rids ) { > > > >> my $rc = $factory->retrieve_blast($rid); > > > >> if( !ref($rc) ) { > > > >> if( $rc < 0 ) { > > > >> print "removing rid as rc is < 0"; > > > >> $factory->remove_rid($rid); > > > >> } > > > >> print STDERR "." if ( $v > 0 ); > > > >> sleep 5; > > > >> } else { > > > >> my $result = $rc->next_result(); > > > >> #save the output > > > >> print "saving to file"; > > > >> my $filename = "contig_236.out"; # > > $result->query_name()."\.out"; > > > >> $factory->save_output($filename); > > > >> $factory->remove_rid($rid); > > > >> print "\nQuery Name: ", $result->query_name(), > > "\n"; > > > >> while ( my $hit = $result->next_hit ) { > > > >> next unless ( $v > 0); > > > >> print "\thit name is ", $hit->name, "\n"; > > > >> while( my $hsp = $hit->next_hsp ) { > > > >> print "\t\tscore is ", $hsp->score, "\n"; > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> > > > >> But when I run this, I get an error in html format which > > says "Cannot > > > >> accept request, error code: -103". Attaching the error > > file for reference. > > > >> Can you please help me with debugging this error? Your > > help is much > > > >> appreciated. > > > >> > > > >> Also, informing about the previous error that I fixed by > > adding this line: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; The error that > > > >> I was getting prior to adding this line was : > > > >> --------------------- WARNING --------------------- > > > >> MSG:

An error has > > occurred on the > > > >> server, The server is unable to format right now, please > > try again in a few > > > >> minutes. If the problem (Informational Message: No > > alias or index file > > > >> found for protein database [nr/nt] in search path > > > >> > > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > > RID: > > > >> 4CF5MY9101P

> > > >> > > > >> It kinda took me a while to find out the 2 > > requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > > >> > > > >> # 1) set your database like this: > > > >> -database => 'cdsearch/cdd', # c.f. > > > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > > >> > > > >> > > > >> # 2) add this line before submitting the job: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'rpsblast'; > > > >> > > > >> I think it will be great if you can add this to the > > synopsis section of > > > >> RemoteBlast.pm > > > >> > > > >> Thanks, > > > >> Sheetal > > > >> > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > From y-bushmanova at northwestern.edu Fri Jul 23 14:54:19 2010 From: y-bushmanova at northwestern.edu (Yulia Bushmanova) Date: Fri, 23 Jul 2010 13:54:19 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E26F.4020103@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> Message-ID: <4C49E55B.6000509@northwestern.edu> Sorry, first email had wrong file attached Yulia Yulia Bushmanova wrote: > Hi All, > > I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and > got following error: > > not well-formed (invalid token) at line 32, column 48, byte 3095 at > /usr/lib/perl5/XML/Parser.pm line 187 > > Looks like parser complains on the copyright sign, if I manually > remove it from file parsing goes fine. XML::Parser is version 2.36. > > Any ideas on how to deal with this error? > > Thanks in advance, > Yulia -------------- next part -------------- A non-text attachment was scrubbed... Name: allRefs_07232010.xml Type: text/xml Size: 42911 bytes Desc: not available URL: From David.Messina at sbc.su.se Fri Jul 23 15:00:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 13:00:07 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> Message-ID: <9C35A675-7A6C-4A33-8826-443CD4E5E541@sbc.su.se> Cool, thanks for the pointer to perlbrew! Dave From cjfields at illinois.edu Fri Jul 23 15:08:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 14:08:03 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E55B.6000509@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> <4C49E55B.6000509@northwestern.edu> Message-ID: <105D6D53-1465-44ED-BA6A-B2D642F09BA9@illinois.edu> You should file this as a bug, along with the output. My guess is it has to do with character encoding, but not sure. chris On Jul 23, 2010, at 1:54 PM, Yulia Bushmanova wrote: > Sorry, first email had wrong file attached > > Yulia > > Yulia Bushmanova wrote: >> Hi All, >> >> I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and got following error: >> >> not well-formed (invalid token) at line 32, column 48, byte 3095 at /usr/lib/perl5/XML/Parser.pm line 187 >> >> Looks like parser complains on the copyright sign, if I manually remove it from file parsing goes fine. XML::Parser is version 2.36. >> >> Any ideas on how to deal with this error? >> >> Thanks in advance, >> Yulia > > > > > > > 20643054 > > 2010 > 7 > 20 > >
> > 1542-0086 > > 99 > 2 > > 2010 > Jul > 21 > > > Biophysical journal > > Bimodal Analysis Reveals a General Scaling Law Governing Nondirected and Chemotactic Cell Motility. > > 367-376 > > > Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a nondirected fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses. Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multiscale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both nondirected and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines, indicating that the coupling of reorientation and persistence holds across species and making it possible to describe the complexity of cell motility in a surprisingly general and simple manner. With this new perspective, we analyzed the motility of Dictyostelium mutants, and found four in which the coupling between two modes was altered. Our results point to a fundamental underlying principle, described by a simple scaling law, unifying mechanisms of eukaryotic cell motility at several scales. > Copyright ? 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. > > Department of Pharmacology, Vanderbilt University, Nashville, Tennessee. > > > Gruver > J Scott > JS > > > Potdar > Alka A > AA > > > Jeon > Junhwan > J > > > Sai > Jiqing > J > > > Anderson > Bridget > B > > > Webb > Donna > D > > > Richmond > Ann > A > > > Quaranta > Vito > V > > > Cummings > Peter T > PT > > > Chung > Chang Y > CY > > > ENG > > JOURNAL ARTICLE > >
> > Biophys J > 0370626 > 0006-3495 > > > > > > 2009 > 12 > 17 > > > 2010 > 3 > 9 > > > 2010 > 3 > 11 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > ppublish > > S0006-3495(10)00710-1 > 10.1016/j.bpj.2010.03.073 > 20643054 > > > > > > > > 20640912 > > 2010 > 7 > 19 > >
> > 1420-9071 > > > 2010 > Jul > 18 > > > Cellular and molecular life sciences : CMLS > > Redundant and unique roles of coronin proteins in Dictyostelium. > > > > > Dictyostelium discoideum harbors a short (CRN12) and a long coronin (CRN7) composed of one and two beta-propellers, respectively. They are primarily present in the cell cortex and cells lacking CRN12 (corA (-)) or CRN7 (corB (-)) have defects in actin driven processes. We compared the characteristics of a mutant cell line (corA (-) /corB (-)) lacking CRN12 and CRN7 with the single mutants focusing on cytokinesis, phagocytosis, chemotaxis and development. Cytokinesis, uptake of small particles, and developmental defects were not enhanced in the corA (-) /corB (-) strain as compared to the single mutants, whereas motility and phagocytosis of yeast particles were more severely impaired. It appears that although both proteins affect the same processes they do not act in a redundant manner. Rather, they often act antagonistically, which is in accordance with their proposed roles in the actin cytoskeleton where CRN12 acts in actin disassembly whereas CRN7 stabilizes actin filaments and protects them from disassembly. > > Institute for Biochemistry I, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931, Cologne, Germany. > > > Shina > Maria C > MC > > > M?ller-Taubenberger > Annette > A > > > Unal > Can > C > > > Schleicher > Michael > M > > > Steinert > Michael > M > > > Eichinger > Ludwig > L > > > M?ller > Rolf > R > > > Blau-Wasser > Rosemarie > R > > > Gl?ckner > Gernot > G > > > Noegel > Angelika A > AA > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 18 > >
> > Cell Mol Life Sci > 9705402 > 1420-682X > > > > > > 2010 > 2 > 3 > > > 2010 > 7 > 5 > > > 2010 > 5 > 23 > > > 2010 > 7 > 18 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 10.1007/s00018-010-0455-y > 20640912 > > > > > > > > 20639697 > > 2010 > 7 > 19 > >
> > 1554-8635 > > 6 > 6 > > 2010 > Aug > 22 > > > Autophagy > > A second signal for autophagic cell death? > > > > > Dictyostelium cells in monolayers in vitro lend themselves well to a study of autophagic cell death (ACD). There is no apoptosis machinery in the protist Dictyostelium, no caspase nor Bcl-2 family members (except a paracaspase whose inactivation does not alter cell death), thus there is no apoptosis that could interfere with, or substitute for, nonapoptotic cell death. Also, Dictyostelium, a eukaryote, has a haploid genome, which facilitates random insertional mutagenesis. > > Centre d'Immunologie de Marseille-Luminy, Facult? des Sciences de Luminy, Aix Marseille Universit?, Marseille, France; Institut National de la Sant? et de la Recherche M?dicale U631, Marseille, France; Centre National de la Recherche Scientifique Unit? Mixte de Recherche, Marseille, France. > > > Giusti > Corinne > C > > > Luciani > Marie-Fran?oise > MF > > > Golstein > Pierre > P > > > ENG > > JOURNAL ARTICLE > > > 2010 > 8 > 22 > >
> > Autophagy > 101265188 > 1554-8627 > > > > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 12750 > 20639697 > > > > > > > > 20626455 > > 2010 > 7 > 19 > >
> > 1462-2920 > > > 2010 > Jul > 7 > > > Environmental microbiology > > The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa. > > > > > Summary The capacity of a bacterial pathogen to produce a disease in a treated host depends on the former's virulence and resistance to antibiotics. Several scattered pieces of evidence suggest that these two characteristics can be influenced by bacterial metabolism. This potential relationship is particularly important upon infection of a host, a situation that demands bacteria adapt their physiology to their new environment, making use of newly available nutrients. To explore the potential cross-talk between bacterial metabolism, antibiotic resistance and virulence, a Pseudomonas aeruginosa model was used. This species is an important opportunistic pathogen intrinsically resistant to many antibiotics. The role of Crc, a global regulator that controls the metabolism of carbon sources and catabolite repression in Pseudomonas, was analysed to determine its contribution to the intrinsic antibiotic resistance and virulence of P. aeruginosa. Using proteomic analyses, high-throughput metabolic tests and functional assays, the present work shows the virulence and antibiotic resistance of this pathogen to be linked to its physiology, and to be under the control (directly or indirectly) of Crc. A P. aeruginosa strain lacking the Crc regulator showed defects in type III secretion, motility, expression of quorum sensing-regulated virulence factors, and was less virulent in a Dictyostelium discoideum model. In addition, this mutant strain was more susceptible to beta-lactams, aminoglycosides, fosfomycin and rifampin. Crc might therefore be a good target in the search for new antibiotics. > > Departamento de Biotecnolog?a Microbiana, Centro Nacional de Biotecnolog?a, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain. > > > Linares > Juan F > JF > > > Moreno > Renata > R > > > Fajardo > Alicia > A > > > Mart?nez-Solano > Laura > L > > > Escalante > Ricardo > R > > > Rojo > Fernando > F > > > Mart?nez > Jos? L > JL > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 07 > >
> > Environ Microbiol > 100883692 > 1462-2912 > > > > > > 2010 > 7 > 15 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > aheadofprint > > EMI2292 > 10.1111/j.1462-2920.2010.02292.x > 20626455 > > > > > > > > 20624437 > > 2010 > 7 > 20 > >
> > 1873-5169 > > > 2010 > Jul > 16 > > > Peptides > > Synthesis and biological activity of peptides equivalent to the IP22 repeat motif found in proteins from Dictyostelium and Mimivirus. > > > > > A novel IP22 repeat motif of unknown function was discovered previously that comprises almost the entire structure of cmbB, a calmodulin-binding protein from Dictyostelium discoideum. An analysis of over 2000 IP22 repeats across 130 different proteins from different species allowed us to define a prototypical IP22 repeat: I/LPxxhxxhxhxxxhxxxhxxxx (where L=leucine, I=isoleucine, h=any hydrophobic amino acid, x=any amino acid). Here we describe the synthesis of three peptide variants of the IP22 motif: IP22-1 (IPNSVTSLKFGDGFNQPLTPGT; 22aa); IP22-2 (LPSTLKTISLSNSTDKKIFKNS; 22aa); and, IP22-3 (IPKSLRSLFLGKGYNQPLEF; 20aa) plus a control peptide from the N-term of cmbB (HNMNPFSPQLDEKKNSHIVEY; 21aa). The structure and purity of synthesized peptides were verified by HPLC and mass spectrometry. The peptides all dose-dependently enhanced random cell motility and cAMP-mediated chemotaxis in Dictyostelium but IP22-3 was most effective peaking in activity around 50muM. Fluorescein isothiocyanate (FITC)-conjugated IP22 peptides did not penetrate cells suggesting these peptides affect cell motility via cell surface interactions. Treatment of cells with FITC-IP22 peptides also led to enhanced cell motility equivalent to the non-conjugated peptides. Treatment of IP22-3-stimulated cells with 50muM LY294002, 20muM quinacrine or both suggests that IP22-3 requires both phosphoinositol 3-kinase and phospholipase A2 signaling to elicit its effects, a mechanism unique from EGFL motility enhancing peptides. The mechanism of action and potential uses of IP22 repeat peptides are discussed. > Copyright ? 2010. Published by Elsevier Inc. > > Department of Cell and Systems Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada, L5L 1C6; Department of Biology, University of Toronto at Mississauga, 3359 Mississauga rd. N., Mississauga, Ontario, Canada, L5L 1C6. > > > Catalano > Andrew > A > > > Luo > Wei > W > > > Wang > Yali > Y > > > O'Day > Danton H > DH > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 16 > >
> > Peptides > 8008690 > 0196-9781 > > > > > > 2010 > 6 > 22 > > > 2010 > 7 > 3 > > > 2010 > 7 > 5 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > aheadofprint > > S0196-9781(10)00300-1 > 10.1016/j.peptides.2010.07.005 > 20624437 > > > > > > > > 20617172 > > 2010 > 07 > 09 > >
> > 1553-7404 > > 6 > > 2010 > > > PLoS genetics > PLoS Genet. > > Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum. > > e1001013 > > > Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle. > > Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America. > > > Flowers > Jonathan M > JM > > > Li > Si I > SI > > > Stathos > Angela > A > > > Saxer > Gerda > G > > > Ostrowski > Elizabeth A > EA > > > Queller > David C > DC > > > Strassmann > Joan E > JE > > > Purugganan > Michael D > MD > > > eng > > Journal Article > Research Support, U.S. Gov't, Non-P.H.S. > > > 2010 > 07 > 01 > >
> > United States > PLoS Genet > 101239074 > 1553-7390 > > IM > PMC2895654 > > > > > 2010 > 3 > 15 > > > 2010 > 6 > 1 > > > 2010 > 7 > 1 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > epublish > > 10.1371/journal.pgen.1001013 > 20617172 > PMC2895654 > > > > > > > > 20610381 > > 2010 > 7 > 8 > >
> > 1083-351X > > > 2010 > Jul > 7 > > > The Journal of biological chemistry > > Expression of actin Tyr53Ala in Dictyostelium disrupts the cytoskeleton and inhibits intracellular and intercellular chemotactic-signaling. > > > > > We showed previously that phosphorylation of Tyr-53, or its mutation to Ala, inhibits actin polymerization in vitro with formation of aggregates of short filaments, and that expression of Y53A-actin in Dictyostelium blocks differentiation and development at the mound stage (Liu et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13694-13699; Liu et al. (2010) J. Biol. Chem. 285, 9729-9739). We now show that expression of Y53A-actin, which does not affect cell growth, phagocytosis or pinocytosis, inhibits the formation of head-to-tail cell streams during cAMP-induced aggregation, although individual amoebae chemotax normally. We show that expression of Y53A-actin causes a 50% reduction of cell-surface cAMP-receptors, and inhibits cAMP-induced increases in adenylyl cyclase A activity, phosphorylation of ERK2 and actin polymerization. Trafficking of vesicles containing adenylyl cyclase A to the rear of the cell and secretion of the ACA-vesicles are also inhibited. The actin cytoskeleton of cells expressing Y53A-actin is characterized by numerous short filaments, and bundled and aggregated filaments similar to the structures formed by copolymerization of purified Y53A-actin and wild-type actin in vitro. This disorganized actin cytoskeleton may be responsible for the inhibition of intracellular and intercellular cAMP signaling in cells expressing F-Y/A-actin. > > NHLBI, NIH, United States; > > > Shu > Shi > S > > > Liu > Xiong > X > > > Kriebel > Paul W > PW > > > Hong > Myoung-Soon > MS > > > Daniels > Mathew P > MP > > > Parent > Carole A > CA > > > Korn > Edward D > ED > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 7 > >
> > J Biol Chem > 2985121R > 0021-9258 > > > > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > aheadofprint > > M110.116277 > 10.1074/jbc.M110.116277 > 20610381 > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Fri Jul 23 19:04:38 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 23 Jul 2010 19:04:38 -0400 Subject: [Bioperl-l] reroot looses branch information Message-ID: Hi, I'm playing with some tree methods from Bio::Tree::TreeFunctionI and I found that Bio::Tree::TreeFunctionI::reroot looses the bootstrap support for the branch leading to the ancestor of the new root. Therefore, when calling reroot, I'm using code like my $ancestor = $newroot->ancestor; my $support = $newroot->bootstrap if (defined $ancestor); $tree->reroot($newroot); $ancestor->bootstrap($support) if (defined $support && defined $ancestor); There seems to be some code in reroot() to prevent that but I don't know why this is happening... Could you please check and fix that? Cheers, Robson From jason.stajich at gmail.com Sat Jul 24 12:41:30 2010 From: jason.stajich at gmail.com (Jason Stajich) Date: Sat, 24 Jul 2010 09:41:30 -0700 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <1125612054.776980.1279892924891.JavaMail.root@zimbra> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> Message-ID: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Hi. You should ask questions to the list. There are many who can answer your question there. In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. -Jason. Sent from my iPod On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > Hi Jason Stajich, > > I am using Bioperl and it is very useful. I have a question about > Bio::DB::GenBank. > This is a simple code. > > -------------------------- > > $db = Bio::DB::GenBank->new(); > @ids = ("LOC441435", "X78121"); > foreach $id (@ids){ > $seqobj = $db->get_Seq_by_id($id); > $seqstr = $seqobj->seq(); > print "$>id\n$seqstr\n"; > } > > -------------------------- > > If there is no entry for an ID, I would like to skip it and to get > next one. But this code stops running when an ID does not exist in > genbank. > How can I solve this problem? > > Thanks. > Hongseok Tae > From cjfields at illinois.edu Sat Jul 24 13:00:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 24 Jul 2010 12:00:24 -0500 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Message-ID: <9F83881D-6C9C-4996-95DF-D98C140DC3EB@illinois.edu> Any reason not to use a stream here? my $io = $db->get_Stream_by_id(\@ids); while (my $seq = $stream->next_seq) { # do stuff here } chris On Jul 24, 2010, at 11:41 AM, Jason Stajich wrote: > Hi. You should ask questions to the list. There are many who can answer your question there. > > In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. > > You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. > -Jason. > Sent from my iPod > > On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > >> Hi Jason Stajich, >> >> I am using Bioperl and it is very useful. I have a question about Bio::DB::GenBank. >> This is a simple code. >> >> -------------------------- >> >> $db = Bio::DB::GenBank->new(); >> @ids = ("LOC441435", "X78121"); >> foreach $id (@ids){ >> $seqobj = $db->get_Seq_by_id($id); >> $seqstr = $seqobj->seq(); >> print "$>id\n$seqstr\n"; >> } >> >> -------------------------- >> >> If there is no entry for an ID, I would like to skip it and to get next one. But this code stops running when an ID does not exist in genbank. >> How can I solve this problem? >> >> Thanks. >> Hongseok Tae >> > _______________________________________________ > 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 Jul 25 00:38:25 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jul 2010 00:38:25 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 Message-ID: Hi All, Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- MAJ From david.breimann at gmail.com Sun Jul 25 08:17:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 15:17:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") Message-ID: Hi, I'm using bp_genbank2gff3.pl and seems to work fine, but when I use the -y (split) option it always gives an error on the very last line of the genbank, whch is actually "//": For example, Can't use an undefined value as a symbol reference at /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. What's the problem? Thanks, Dave From dan.bolser at gmail.com Sun Jul 25 09:23:35 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 14:23:35 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? Message-ID: Hi all, The following bug report boils down to this question: How should two sequence objects be compared for identity? Does the object override 'eq' or implement an 'identical' method? I found the following apparent bug in Contig.pm while executing the documented 'SYNOPSIS' code: #!/usr/bin/perl -w use strict; use Bio::Assembly::Contig; my $c = Bio::Assembly::Contig-> new( -id => '1' ); my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' ); my $ls_coord = Bio::SeqFeature::Generic-> new( -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); $c->set_seq_coord( $ls_coord, $ls ); Gives the following WARNINGs: --------------------- WARNING --------------------- MSG: Adding sequence r1, which has already been added --------------------------------------------------- --------------------- WARNING --------------------- MSG: Replacing one sequence [r1] --------------------------------------------------- It seems to be a bug in the documented behaviour of set_seq_coord: "If the sequence was previously added using add_seq, its coordinates are changed/set. Otherwise, add_seq is called and the sequence is added to the contig." The offending line in that function seems to be: if( ... && ($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { ... } $self->add_seq($seq); which compares the *passed* sequence object to the sequence string for the *stored* sequence object of the same name. This comparison is always fails if I understood correctly, therefore set_seq_coord always spews warnings if called after add_seq. Out of curiosity, how come I can't just say: my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); I hope the above report can be of some use. Sincerely, Dan. From robfsouza at gmail.com Sun Jul 25 10:42:35 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sun, 25 Jul 2010 10:42:35 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Hi Dan, It is been a long time since I last loooked at this but, if I remember correctly, the point is that Bio:: On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: > The following bug report boils down to this question: > How should two sequence objects be compared for identity? Does the > object override 'eq' or implement an 'identical' method? I think an 'identical' or 'equal' method would be the best alternative since having a full method call would allow passing arguments like '-mode => "complete"' to check all sequence features and annotations if they exist and '-mode => "basic"' to check id() and seq() values. Bio::Assembly::Contig depends mostly on the last one, although only id() is tracked most of the time (because of the internal hashes). > I found the following apparent bug in Contig.pm while executing the > documented 'SYNOPSIS' code: [snip] > It seems to be a bug in the documented behaviour of set_seq_coord: > ? ? ? ?"If the sequence was previously added using add_seq, its > coordinates are changed/set. ?Otherwise, add_seq is called and the > sequence is added to the contig." In fact, it should not print warnings all the time.... > The offending line in that function seems to be: > ?if( ... && > ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { > ? ? ? ? ?... > ?} > ?$self->add_seq($seq); > which compares the *passed* sequence object to the sequence string for > the *stored* sequence object of the same name. This comparison is > always fails if I understood correctly, therefore set_seq_coord always > spews warnings if called after add_seq. Not the sequence string, but the objects themselves, i.e. the string perl uses to represent Bio::LocatableSeq objects... it is a memory based version of identical() :) > Out of curiosity, how come I can't just say: > my $ls = Bio::LocatableSeq-> > ?new( -seq ? ? ?=> 'ACCG-T', > ? ? ? -id ? ? ? => 'r1', > ? ? ? -alphabet => 'dna' > ? ? ? -start ? ?=> 3, > ? ? ? -end ? ? ?=> 8, > ? ? ? -strand ? => 1 > ? ? ); > $c->add_seq( $ls ); Oh, I don't remember but it was either a bad design decision I made 8 years ago to acommodate the Bio::Align::AlignI interface or a problem with Bio::SeqFeature::Collection at that time. Whatever the case, it would be nice to change it... you just need to create a Bio::SeqFeature::Generic when add_seq is called. I just won't have time to do it myself so feel free to act... Best, Robson > I hope the above report can be of some use. > > Sincerely, > Dan. > _______________________________________________ > 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 Sun Jul 25 12:35:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:35:42 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Cheers for the clarification Robson. How come the 'SYNOPSIS' code does produce warnings about replacing the seq? (the workaround is easy enough, don't add_seq, but still...) Since you said 'feel free to act', I have been faffing around here: http://github.com/dbolser/bioperl-live I'm not really sure if that is so useful, please advise. Thanks again for help, Dan. P.S. How come you are not in irc://irc.freenode.net/#bioperl ;-) On 25 July 2010 15:42, Robson de Souza wrote: > Hi Dan, > > It is been a long time since I last loooked at this but, if I remember > correctly, the point is that Bio:: > > On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >> The following bug report boils down to this question: >> How should two sequence objects be compared for identity? Does the >> object override 'eq' or implement an 'identical' method? > > I think an 'identical' or 'equal' method would be the best alternative > since having a full method call would allow passing arguments like > '-mode => "complete"' to check all sequence features and annotations > if they exist and '-mode => "basic"' to check id() and seq() values. > Bio::Assembly::Contig depends mostly on the last one, although only > id() is tracked most of the time (because of the internal hashes). > >> I found the following apparent bug in Contig.pm while executing the >> documented 'SYNOPSIS' code: > [snip] >> It seems to be a bug in the documented behaviour of set_seq_coord: >> ? ? ? ?"If the sequence was previously added using add_seq, its >> coordinates are changed/set. ?Otherwise, add_seq is called and the >> sequence is added to the contig." > > In fact, it should not print warnings all the time.... > >> The offending line in that function seems to be: >> ?if( ... && >> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >> ? ? ? ? ?... >> ?} >> ?$self->add_seq($seq); >> which compares the *passed* sequence object to the sequence string for >> the *stored* sequence object of the same name. This comparison is >> always fails if I understood correctly, therefore set_seq_coord always >> spews warnings if called after add_seq. > > Not the sequence string, but the objects themselves, i.e. the string > perl uses to represent Bio::LocatableSeq objects... it is a memory > based version of identical() :) > >> Out of curiosity, how come I can't just say: >> my $ls = Bio::LocatableSeq-> >> ?new( -seq ? ? ?=> 'ACCG-T', >> ? ? ? -id ? ? ? => 'r1', >> ? ? ? -alphabet => 'dna' >> ? ? ? -start ? ?=> 3, >> ? ? ? -end ? ? ?=> 8, >> ? ? ? -strand ? => 1 >> ? ? ); >> $c->add_seq( $ls ); > > Oh, I don't remember but it was either a bad design decision I made 8 > years ago to acommodate the Bio::Align::AlignI interface or a problem > with Bio::SeqFeature::Collection at that time. Whatever the case, it > would be nice to change it... you just need to create a > Bio::SeqFeature::Generic when > add_seq is called. I just won't have time to do it myself so feel free to act... > > Best, > Robson > >> I hope the above report can be of some use. >> >> Sincerely, >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From dan.bolser at gmail.com Sun Jul 25 12:40:21 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:40:21 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? Message-ID: Which objects implement SeqFeatureI, and how should I find that info? Sorry for the gratuitous noobs. Cheers, Dan. From genehack at genehack.org Sun Jul 25 14:06:55 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:06:55 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> (This is in reference to: ; sorry I'm not responding to the original message but I wasn't on the list at that point.) There are really two issues being reported here. First, bp_seqfeature_gff3.PLS throws the following error when used with Bio::SeqFeature::Store::DBI::SQLite: > Can't locate object method "gff3_string" via package "Bio::SeqFeature::Generic" at /Users/jhannah/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS line 58. Second, when called on a database that's been built with '$db->no_blobs(1)', the output doesn't actually include any features. I've got a fix for the first bug in . (I've submitted a pull request for that branch to the 'bioperl' user.) Basically, when looping over the feature objects in bp_seqfeature_gff3.PLS, we introspect each one to find out if it supports the gff3_string() or gff_string() methods, and either call the appropriate one or throw an exception. (I considered just calling gff_string() instead of doing the introspection, since (a) that's the interface documented in SeqFeatureI and (b) SeqFeature::Lite, which is the only thing that currently implements gff3_string() _also_ implements gff_string(), which recalls gff3_string() when appropriate, but in the end decided that this way preserves the original intent of the script as much as possible...) I'm working on something that may be a fix for the second issue as well, but thought I'd throw this first bit out for comments, being as this is the first change I've contributed back to the project. thanks, john. From genehack at genehack.org Sun Jul 25 14:36:07 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:36:07 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> Message-ID: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> On Jul 25, 2010, at 2:06 PM, John Anderson wrote: > Second, when called on a database that's been built with '$db->no_blobs(1)', the output [ snip ] I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. (A pull request for this change has been sent to the 'bioperl' user on Github.) thanks, john. From genehack at genehack.org Sun Jul 25 14:58:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:58:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > the -y (split) option it always gives an error on the very last line > of the genbank, whch is actually "//": > > For example, > > Can't use an undefined value as a symbol reference at > /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > > What's the problem? > I filed a bug for you; it's #3124 and can be seen at The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS > index 1216810..6bdae9d 100755 > --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > @@ -654,7 +654,7 @@ for my $file ( @files ) { > } > > ## FIXME for piped output w/ split FA files ... > - close($lumpfa_fh); > + close($lumpfa_fh) if $lumpfa_fh; > if (!$split && $outfa && $lump_fh) { > print $lump_fh "##FASTA\n"; # GFF3 spec > open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > > chrs, john. From cjfields at illinois.edu Sun Jul 25 15:18:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:18:41 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> Message-ID: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> On Jul 25, 2010, at 1:36 PM, John Anderson wrote: > On Jul 25, 2010, at 2:06 PM, John Anderson wrote: >> Second, when called on a database that's been built with '$db->no_blobs(1)', the output > [ snip ] > > I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. > > I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. > > (A pull request for this change has been sent to the 'bioperl' user on Github.) > > thanks, > john. On this one (in Bio::DB::SeqFeature::DBI::mysql): if ( $typeid and $db_seqid and $start and $end and $strand ) { # then we're good... } else { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Changing this to the following should work and is more direct: if ( !defined($typeid) || !defined($db_seqid) || !defined($start) || !defined($end) || !defined($strand) ) { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Might even work shortening to a grep: if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} chris From cjfields at illinois.edu Sun Jul 25 15:20:09 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:20:09 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Pull request was merged into master branch of bioperl-live. Thanks! Oddly, pull requests aren't coming through via the mail list, I'll look into the issue. chris On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use >> the -y (split) option it always gives an error on the very last line >> of the genbank, whch is actually "//": >> >> For example, >> >> Can't use an undefined value as a symbol reference at >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. >> >> What's the problem? >> > > I filed a bug for you; it's #3124 and can be seen at > > The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> index 1216810..6bdae9d 100755 >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> @@ -654,7 +654,7 @@ for my $file ( @files ) { >> } >> >> ## FIXME for piped output w/ split FA files ... >> - close($lumpfa_fh); >> + close($lumpfa_fh) if $lumpfa_fh; >> if (!$split && $outfa && $lump_fh) { >> print $lump_fh "##FASTA\n"; # GFF3 spec >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; >> >> > > chrs, > john. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Sun Jul 25 15:48:22 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 15:48:22 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: On Jul 25, 2010, at 3:18 PM, Chris Fields wrote: > On this one (in Bio::DB::SeqFeature::DBI::mysql): > > if ( $typeid and $db_seqid and $start and $end and $strand ) { Yeah, sorry, that sort of bugged me too, but once I got into testing stuff I forgot to go back and clean it up... > Might even work shortening to a grep: > > if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} Ended up with: # if we weren't called with all the params, pull those out of the database too if ( not ( grep { defined($_) } ( ... ))) { ... } because having the negation buried inside the grep block seemed confusing... I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) j. From david.breimann at gmail.com Sun Jul 25 15:52:53 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 22:52:53 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. Thanks! On Sun, Jul 25, 2010 at 10:20 PM, Chris Fields wrote: > Pull request was merged into master branch of bioperl-live. Thanks! > > Oddly, pull requests aren't coming through via the mail list, I'll look > into the issue. > > chris > > On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > > > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > > > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > >> the -y (split) option it always gives an error on the very last line > >> of the genbank, whch is actually "//": > >> > >> For example, > >> > >> Can't use an undefined value as a symbol reference at > >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > >> > >> What's the problem? > >> > > > > I filed a bug for you; it's #3124 and can be seen at < > http://bugzilla.open-bio.org/show_bug.cgi?id=3124> > > > > The following patch fixes it for me; it can be found in < > http://github.com/genehack/bioperl-live/tree/topic/bug-3124>. I've sent a > pull request for this change. > > > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS > b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> index 1216810..6bdae9d 100755 > >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> @@ -654,7 +654,7 @@ for my $file ( @files ) { > >> } > >> > >> ## FIXME for piped output w/ split FA files ... > >> - close($lumpfa_fh); > >> + close($lumpfa_fh) if $lumpfa_fh; > >> if (!$split && $outfa && $lump_fh) { > >> print $lump_fh "##FASTA\n"; # GFF3 spec > >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > >> > >> > > > > chrs, > > john. > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From genehack at genehack.org Sun Jul 25 16:05:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 16:05:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <139B16C1-C964-4C9A-AB7F-A6566749B215@genehack.org> On Jul 25, 2010, at 3:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Or you could just change the one line in the script yourself; that was the only change. > Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Could you send me (not the list, just me) an input file that produces this problem? > Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. It looks like the '-n' option should do that, but it currently throws a few more errors of the same general type as you were seeing before -- let me look at those... j. From David.Messina at sbc.su.se Sun Jul 25 16:34:42 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 25 Jul 2010 14:34:42 -0600 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> On Jul 25, 2010, at 13:48, John Anderson wrote: > > I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) You've probably seen this, right? http://www.bioperl.org/wiki/Bioperl_Best_Practices Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) Thanks for all your work on this, John! Dave From biopython at maubp.freeserve.co.uk Sun Jul 25 17:10:30 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 25 Jul 2010 22:10:30 +0100 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: On Sun, Jul 25, 2010 at 8:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view > to use to updated version should I first update my clone of bioperl-live > (git pull?) then go through the whole build and install again? > > Second, I have just noticed that bp_genbank2gff3.pl returns an error when > given a circular genome with a feature that spans the "end" of the genome > (e.g., assume the genome size is 1000np and a feature spans > join(900..1000,1..100). The GFF3 spec has recently been updated to cover circular genomes explicitly - this script probably needs updating in light of this. Peter From hlapp at drycafe.net Sun Jul 25 17:26:39 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 25 Jul 2010 17:26:39 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: Message-ID: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > Hi All, > Our BP poster from the conference is available on SlideShare (search > BioPerl ISMB 2010) and on my wiki homepage. Enjoy- If anyone was wondering about the URL: http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 Mark - were you going to post a news item on this? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sun Jul 25 19:05:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:05:49 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> Message-ID: <9F8B93B0-40B4-4D36-AFC8-42AB0F640E80@illinois.edu> On Jul 25, 2010, at 3:34 PM, Dave Messina wrote: > On Jul 25, 2010, at 13:48, John Anderson wrote: >> >> I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) > > You've probably seen this, right? > > http://www.bioperl.org/wiki/Bioperl_Best_Practices > > Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) > > Thanks for all your work on this, John! > > > > Dave Agreed, thanks John. I'll pull this into a local branch and test, then pull in if everything's okay. chris From cjfields at illinois.edu Sun Jul 25 19:09:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:22 -0500 Subject: [Bioperl-l] BOSC 2010 BioPerl slides Message-ID: <94B38B72-EC74-49AA-B8E6-7E0E0ABDEBFA@illinois.edu> Just a note that, along with Mark's poster, I gave a smallish update on BioPerl at BOSC 2010: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Feedback welcome! chris From cjfields at illinois.edu Sun Jul 25 19:09:35 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:35 -0500 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> Message-ID: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > > On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >> Hi All, >> Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > > If anyone was wondering about the URL: > > http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > > Mark - were you going to post a news item on this? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== We could do this along with posting the slides for the BOSC BioPerl talk: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl chris From cjfields at illinois.edu Sun Jul 25 19:11:06 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:11:06 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <9FB52BF8-532C-4FA2-A590-4ECDA9700E8B@illinois.edu> On Jul 25, 2010, at 4:10 PM, Peter wrote: > On Sun, Jul 25, 2010 at 8:52 PM, David Breimann > wrote: >> Thank you guys. I'm quite new to all this github stuff, so in order to view >> to use to updated version should I first update my clone of bioperl-live >> (git pull?) then go through the whole build and install again? >> >> Second, I have just noticed that bp_genbank2gff3.pl returns an error when >> given a circular genome with a feature that spans the "end" of the genome >> (e.g., assume the genome size is 1000np and a feature spans >> join(900..1000,1..100). > > The GFF3 spec has recently been updated to cover circular > genomes explicitly - this script probably needs updating in light > of this. > > Peter We need to add a few tests for circular genomes with BioPerl; I'm pretty sure these currently do not work as expected. chris From grapevine.256 at gmail.com Mon Jul 26 00:27:16 2010 From: grapevine.256 at gmail.com (Vidya Oruganti) Date: Mon, 26 Jul 2010 12:27:16 +0800 Subject: [Bioperl-l] Restriction Analysis Message-ID: Dear All, I am interested in knowing if there is a way to perform the restriction analysis module on many sequences at once. Currently I am retrieving sequences of contigs one by one from genbank and performing the restriction analysis individually. This is the script I am using: use Bio::Restriction::Analysis; use Bio::DB::GenBank; use Data::Dumper; use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); $seq = $gb->get_Seq_by_gi('405830'); # GI Number my $ra = Bio::Restriction::Analysis->new(-seq=>$seq); print "There are ", scalar $ra->zero_cutters->each_enzyme, " enzymes that do not cut\n"; printf "\n%-10s%s\n", 'Enzyme', 'Number of Cuts'; my $all_cutters = $ra->cutters; map { printf "%-10s%s\n", $_->name, $ra->cuts_by_enzyme($_->name) } $all_cutters->each_enzyme; I would like to know whether it would be possible to get an array of sequences from genbank instead of just one and run the restriction analysis on all the sequences at one go and get several outputs at once. I have been able to retrieve more than one sequence from genbank but I'm not able to run the analysis on more than one sequence. Thank you From adsj at novozymes.com Mon Jul 26 03:09:54 2010 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 26 Jul 2010 09:09:54 +0200 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> (Chris Fields's message of "Sun, 25 Jul 2010 18:09:35 -0500") References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> Message-ID: <87eieqen25.fsf@topper.koldfront.dk> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> Our BP poster from the conference is available on SlideShare (search >>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Any chance of posting these slides for download somewhere that doesn't require creating an account to do so? Best wishes, Adam, just curious. -- Adam Sj?gren adsj at novozymes.com From avilella at gmail.com Mon Jul 26 05:08:32 2010 From: avilella at gmail.com (Albert Vilella) Date: Mon, 26 Jul 2010 10:08:32 +0100 Subject: [Bioperl-l] Run wrappers for BWA and Samtools In-Reply-To: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> References: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> Message-ID: Hi Mark, First of all, great work. Can I ask if the aim of combining bwa and samtools would be or could be to replicate "maq.pl easyrun" ? Or what would be an alternative for users wanting to do "maq.pl easyrun" for a combination of long and short reads? Cheers, Albert. On Sat, Nov 28, 2009 at 5:23 PM, Mark A. Jensen wrote: > Hi All, > > Run wrappers for the bwa assembler and the samtools suite > are now available as beta in the bioperl-run/trunk. The bwa > wrapper allows you to run a canned assembly pipeline, or > to execute individual bwa components. The assembly pipeline > can return a Bio::Assembly::Scaffold object via the new > Bio::Assembly::IO::sam module in bioperl-live/trunk > (this requires lstein's Bio::DB::Sam, from CPAN). Details at > > http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA > > and, of course, in the pod. > > Cheers, > MAJ > _______________________________________________ > 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 Jul 26 09:38:01 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:38:01 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 Message-ID: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.com > > _______________________________________________ > 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 Jul 26 09:18:56 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:18:56 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Hi Benard, Forwarding to the list for more help for you. You may want to look at the POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to use this module to create an OrthoMCL wrapper. This might be more technical than you want. Maybe a dev on the list would be interested in creating a wrapper using CommandExts. cheers, MAJ ----- Original Message ----- From: "Benard Kulohoma" To: Sent: Wednesday, July 21, 2010 10:58 AM Subject: Inquiry Hi Mark, I just read your bioperl resource on BWA (and here: http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was most helpful. Do you have any idea of how I could use Bioperl to implement OrthoMCL of several bacterial genomes. I would like to find some membrane proteins. Many thanks, Benard PS: I am sorry for spaming/inquiring!! :) -- 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 roy.chaudhuri at gmail.com Mon Jul 26 09:46:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 26 Jul 2010 14:46:49 +0100 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: <4C4D91C9.4090704@gmail.com> Thanks for this Mark. Just in case anyone can't find it, it's here: http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png Roy. On 26/07/2010 14:38, Mark A. Jensen wrote: > missed the list-- > ----- Original Message ----- > From: "Mark A. Jensen" > To: "Adam "Sj?gren"" > Sent: Monday, July 26, 2010 9:37 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > >> There's a png version of the poster on my wiki page >> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >> wiki thinks it should?). Chris, maybe could upload yours to wiki? >> cheers MAJ >> ----- Original Message ----- >> From: "Adam "Sj?gren"" >> To: >> Sent: Monday, July 26, 2010 3:09 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >> >>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> >>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >> >>>>> Our BP poster from the conference is available on SlideShare (search >>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> >>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >> >>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >> >> Any chance of posting these slides for download somewhere that doesn't >> require creating an account to do so? >> >> >> Best wishes, >> >> Adam, just curious. >> >> -- >> Adam Sj?gren >> adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 09:46:38 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:46:38 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: http://bioperl.org/wiki/Mark_Jensen, it is... ----- Original Message ----- From: "Mark A. Jensen" To: "BioPerl List" Sent: Monday, July 26, 2010 9:38 AM Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 10:05:12 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 10:05:12 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4C4D91C9.4090704@gmail.com> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: http://posters.f1000.com/PosterList?posterID=246 ----- Original Message ----- From: "Roy Chaudhuri" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, July 26, 2010 9:46 AM Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > Thanks for this Mark. Just in case anyone can't find it, it's here: > http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png > > Roy. > > On 26/07/2010 14:38, Mark A. Jensen wrote: >> missed the list-- >> ----- Original Message ----- >> From: "Mark A. Jensen" >> To: "Adam "Sj?gren"" >> Sent: Monday, July 26, 2010 9:37 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >>> There's a png version of the poster on my wiki page >>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with >>> uploading >>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>> cheers MAJ >>> ----- Original Message ----- >>> From: "Adam "Sj?gren"" >>> To: >>> Sent: Monday, July 26, 2010 3:09 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>> >>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>> >>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> >>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>> >>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>> >>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>> >>> Any chance of posting these slides for download somewhere that doesn't >>> require creating an account to do so? >>> >>> >>> Best wishes, >>> >>> Adam, just curious. >>> >>> -- >>> Adam Sj?gren >>> adsj at novozymes.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 amackey at virginia.edu Mon Jul 26 10:51:43 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Mon, 26 Jul 2010 10:51:43 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes sense to "wrap" it. See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt -Aaron On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > Hi Benard, > Forwarding to the list for more help for you. You may want to look at the > POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live > distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to > use this module to create an OrthoMCL wrapper. This might be more technical > than you want. Maybe a dev on the list would be interested in creating a > wrapper using CommandExts. > cheers, MAJ > ----- Original Message ----- From: "Benard Kulohoma" < > B.Kulohoma at liverpool.ac.uk> > To: > Sent: Wednesday, July 21, 2010 10:58 AM > Subject: Inquiry > > > Hi Mark, > > I just read your bioperl resource on BWA (and here: > http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was > most helpful. Do you have any idea of how I could use Bioperl to implement > OrthoMCL of several bacterial genomes. I would like to find some membrane > proteins. > > Many thanks, > > Benard > > PS: I am sorry for spaming/inquiring!! :) > > -- > 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. > > > _______________________________________________ > 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 Jul 26 11:05:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 10:05:05 -0500 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: <84B78CA5-5D0E-447C-B507-8FCA18EDA7CB@illinois.edu> Agreed; I'm using it locally. I could see subclassing BLAST (or similar) wrappers specifically for the all-v-all portion of the pipeline (for consistency/flexibility), but I get along w/o that. chris On Jul 26, 2010, at 9:51 AM, Aaron Mackey wrote: > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 maj at fortinbras.us Mon Jul 26 11:07:35 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 11:07:35 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Maybe not in the sense of CommandExts, but a BioPerl module that does the "13 steps" might be very useful. (Not saying anyone should do it :) ) ----- Original Message ----- From: "Aaron Mackey" To: "Mark A. Jensen" Cc: "BioPerl List" ; "Benard Kulohoma" Sent: Monday, July 26, 2010 10:51 AM Subject: Re: [Bioperl-l] Inquiry on OrthoMCL > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Jul 26 11:35:18 2010 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jul 2010 11:35:18 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, I think there are probably several BioPerl classes that implement Bio::SeqFeatureI, like Bio::SeqFeature::Generic. What are you looking for? Scott On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: > Which objects implement SeqFeatureI, and how should I find that info? > > Sorry for the gratuitous noobs. > > Cheers, > Dan. > _______________________________________________ > 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 Mon Jul 26 12:22:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 11:22:54 -0500 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: I've added the PDF version of the BOSC 2010 talk and both the PDF and .ppt versions of the ISMB 2010 BioPerl poster here: http://www.bioperl.org/DIST/presentations/ Just a warning, the PDF of the poster has copyright notices all over it (I'll post a clean one if it's emailed to me!). Mark, did you want to make a blog post about these? chris On Jul 26, 2010, at 9:05 AM, Mark A. Jensen wrote: > Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: > http://posters.f1000.com/PosterList?posterID=246 > ----- Original Message ----- From: "Roy Chaudhuri" > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Monday, July 26, 2010 9:46 AM > Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > > >> Thanks for this Mark. Just in case anyone can't find it, it's here: >> http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png >> >> Roy. >> >> On 26/07/2010 14:38, Mark A. Jensen wrote: >>> missed the list-- >>> ----- Original Message ----- >>> From: "Mark A. Jensen" >>> To: "Adam "Sj?gren"" >>> Sent: Monday, July 26, 2010 9:37 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>>> There's a png version of the poster on my wiki page >>>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >>>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>>> cheers MAJ >>>> ----- Original Message ----- >>>> From: "Adam "Sj?gren"" >>>> To: >>>> Sent: Monday, July 26, 2010 3:09 AM >>>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>>> >>>> >>>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>>> >>>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>>> >>>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>>> >>>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>>> >>>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>>> >>>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>>> >>>> Any chance of posting these slides for download somewhere that doesn't >>>> require creating an account to do so? >>>> >>>> >>>> Best wishes, >>>> >>>> Adam, just curious. >>>> >>>> -- >>>> Adam Sj?gren >>>> adsj at novozymes.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 >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Mon Jul 26 13:54:22 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Mon, 26 Jul 2010 13:54:22 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: > Thanks again Robson, > > One thing I was going to email the list about is a lack of tests for > ace.pm and phrap.pm ... because of missing libs I'm not running the > sam or the maq tests, so any changes that I'm making to Contig.pm / > Scaffold.pm are not really being tested. > > Do you think anyone on the list (or you) would be able to generate a > few hundred tests to help me start modifying code with confidence? I hope so. I was reading Chris's presentation at BOSC and he mentioned that people are working on the support for the samtools so I believe somebody must have a dataset they could share. > One idea was to actually make Contig.pm implement SeqFeatureI, so that > you could call start and end and seq on the contig (consensus) > directly. > > Here are some notes from IRC... > > 04:00 < dbolser> I think "$contig_object->start" is totally reasonable > 04:01 < dbolser> otherwise its something like > "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" > 04:02 < dbolser> (untested ;-) > 09:01 < genehack> dbolser: i think you've got an argument that there should be; > it's probably going to be a lot easier to do that in > something like Biome (i.e., BioPerl in Moose) Never thought about it... but I can see that could be useful when contigs are part of higher level assemblies, like scaffolds or assembled chromosomes, but you could also achieve this by making Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any reason to prefer the Bio::SeqFeatureI interface? > Any reason not to cc this to the list? Lack of attention. I was so concerned about the answer that I didn't notice I pressed "Reply to" :) Best, Robson > Thanks again. > > All the best, > Dan. > > > > > On 26 July 2010 17:23, Robson de Souza wrote: >> Hi, >> >> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>> Cheers for the clarification Robson. >> >> You are welcome :). Thanks for improving my long abandoned child... :) >> >>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>> seq? (the workaround is easy enough, don't add_seq, but still...) >> >> I don't know. I remember testing it while I develop Contig.pm in >> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >> Did you try ace.pm recently? It uses set_seq_coord and this method >> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >> of previous bug reports on ace.pm regarding unexpected warnings... >> note that set_seq_coord calls remove_seq before adding but prints >> another warning. Compare set_seq_coord to add_seq alone and maybe you >> will figure out what is going on... >> >> Regarding why you can't just add Bio::LocatableSeq objects and have >> add_seq just set the coordinates by itself, I investigated my long >> forgotten code and just realized that the whole problem was that the >> coordinates of a Bio::LocatableSeq object represent the location of >> the object in the original sequence (i.e. unaligned read coordinates) >> instead of its coordinates in the aligned consensus sequence. >> Bio::LocatableSeq issues a warning whenever you try to set the object >> start and end coordinates to the gapped consensus coordinates because >> such coordinates lead to a length shorter than the actual read length: >> >> use Bio::LocatableSeq; >> use Bio::SeqFeature::Collection; >> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >> =>"agggcACT-Gccc", -id=>"uga"); >> my $sfc = Bio::SeqFeature::Collection->new(); >> $sfc->add_features([ $ls ]); >> print $sfc->feature_count,"\t",$ls->length."\n"; >> >> Additionally, Bio::LocatableSeq objects do not support the >> primary_tag() method because they are just Bio::RangeI and not >> Bio::SeqFeatureI objects. These two issues prevented me from using >> Bio::LocatableSeq coordinates to represent gapped consensus >> coordinates but the example code above suggests suppressing >> Bio::LocatableSeq warnings and using the object class >> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >> the need for extra Bio::SeqFeature::Generic objects to store read >> coordinates. >> >>> Since you said 'feel free to act', I have been faffing around here: >>> http://github.com/dbolser/bioperl-live >>> I'm not really sure if that is so useful, please advise. >> >> The comments I made above points to one area where you could have some >> improvements in both memory usage and usability: drop the need for >> additional Bio::SeqFeatureI objects to represent gapped consensus >> coordinates. It would require you to check all Contig.pm methods for >> the use of the "_aligned_coord:$readID" tags (I don't expect to see >> any references to this outside Contig.pm) and change set_seq_coord to >> a method that changes/sets the start and end values of the >> Bio::LocatableSeq objects. >> This might be a bit of work so just go for it if you want and have >> time to experiment. >> >> Another detail: could you please replace references in Contig.pm and >> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >> not exists to the correct Bio::* classes? Somebody changed this to the >> wrong names long ago... >> >>> Thanks again for help, >> >> Well these are my thoughts on the matter. Write again if you decide to >> take this on and are unable to make progress. >> Best, >> Robson >> >>> Dan. >>> >>> >>> P.S. >>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>> >>> >>> On 25 July 2010 15:42, Robson de Souza wrote: >>>> Hi Dan, >>>> >>>> It is been a long time since I last loooked at this but, if I remember >>>> correctly, the point is that Bio:: >>>> >>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>> The following bug report boils down to this question: >>>>> How should two sequence objects be compared for identity? Does the >>>>> object override 'eq' or implement an 'identical' method? >>>> >>>> I think an 'identical' or 'equal' method would be the best alternative >>>> since having a full method call would allow passing arguments like >>>> '-mode => "complete"' to check all sequence features and annotations >>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>> id() is tracked most of the time (because of the internal hashes). >>>> >>>>> I found the following apparent bug in Contig.pm while executing the >>>>> documented 'SYNOPSIS' code: >>>> [snip] >>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>> sequence is added to the contig." >>>> >>>> In fact, it should not print warnings all the time.... >>>> >>>>> The offending line in that function seems to be: >>>>> ?if( ... && >>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>> ? ? ? ? ?... >>>>> ?} >>>>> ?$self->add_seq($seq); >>>>> which compares the *passed* sequence object to the sequence string for >>>>> the *stored* sequence object of the same name. This comparison is >>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>> spews warnings if called after add_seq. >>>> >>>> Not the sequence string, but the objects themselves, i.e. the string >>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>> based version of identical() :) >>>> >>>>> Out of curiosity, how come I can't just say: >>>>> my $ls = Bio::LocatableSeq-> >>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>> ? ? ? -id ? ? ? => 'r1', >>>>> ? ? ? -alphabet => 'dna' >>>>> ? ? ? -start ? ?=> 3, >>>>> ? ? ? -end ? ? ?=> 8, >>>>> ? ? ? -strand ? => 1 >>>>> ? ? ); >>>>> $c->add_seq( $ls ); >>>> >>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>> would be nice to change it... you just need to create a >>>> Bio::SeqFeature::Generic when >>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>> >>>> Best, >>>> Robson >>>> >>>>> I hope the above report can be of some use. >>>>> >>>>> Sincerely, >>>>> Dan. >>>>> _______________________________________________ >>>>> 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 Tue Jul 27 04:53:49 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 09:53:49 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 26 July 2010 16:35, Scott Cain wrote: > Hi Dan, > > I think there are probably several BioPerl classes that implement > Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking > for? A way to find what implements what... something like javadoc for bp. Really I'm looking for a nice 'ontology' of SeqFeatures. I was thinking that Contig.pm should implement Bio::SeqFeatureI. > Scott > > > On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >> Which objects implement SeqFeatureI, and how should I find that info? >> >> Sorry for the gratuitous noobs. >> >> Cheers, >> Dan. >> _______________________________________________ >> 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 dan.bolser at gmail.com Tue Jul 27 05:02:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 10:02:05 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On 26 July 2010 18:54, Robson de Souza wrote: > On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >> Thanks again Robson, >> >> One thing I was going to email the list about is a lack of tests for >> ace.pm and phrap.pm ... because of missing libs I'm not running the >> sam or the maq tests, so any changes that I'm making to Contig.pm / >> Scaffold.pm are not really being tested. >> >> Do you think anyone on the list (or you) would be able to generate a >> few hundred tests to help me start modifying code with confidence? > > I hope so. I was reading Chris's presentation at BOSC and he mentioned > that people are working on the support for the samtools so I believe > somebody must have a dataset they could share. Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because I don't have samtools installed. Also, (quick impression) method coverage is limited (Contig.pm has a lot of methods!). I'll try to write some tests for ace.pm and phrap.pm. >> One idea was to actually make Contig.pm implement SeqFeatureI, so that >> you could call start and end and seq on the contig (consensus) >> directly. >> >> Here are some notes from IRC... >> >> 04:00 < dbolser> I think "$contig_object->start" is totally reasonable >> 04:01 < dbolser> otherwise its something like >> "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" >> 04:02 < dbolser> (untested ;-) >> 09:01 < genehack> dbolser: i think you've got an argument that there should be; >> ? ? ? ? ? ? ? ? ?it's probably going to be a lot easier to do that in >> ? ? ? ? ? ? ? ? ?something like Biome (i.e., BioPerl in Moose) > > Never thought about it... but I can see that could be useful when > contigs are part of higher level assemblies, like scaffolds or > assembled chromosomes, but you could also achieve this by making > Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any > reason to prefer the Bio::SeqFeatureI interface? No. I don't have an overview of how the various objects relate to one another, so any choice is more or less arbitrary. I'll try to write a 'Sequence HOWTO'. Thanks again for help, Dan. >> Any reason not to cc this to the list? > > Lack of attention. I was so concerned about the answer that I didn't > notice I pressed "Reply to" :) > Best, > Robson > >> Thanks again. >> >> All the best, >> Dan. >> >> >> >> >> On 26 July 2010 17:23, Robson de Souza wrote: >>> Hi, >>> >>> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>>> Cheers for the clarification Robson. >>> >>> You are welcome :). Thanks for improving my long abandoned child... :) >>> >>>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>>> seq? (the workaround is easy enough, don't add_seq, but still...) >>> >>> I don't know. I remember testing it while I develop Contig.pm in >>> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >>> Did you try ace.pm recently? It uses set_seq_coord and this method >>> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >>> of previous bug reports on ace.pm regarding unexpected warnings... >>> note that set_seq_coord calls remove_seq before adding but prints >>> another warning. Compare set_seq_coord to add_seq alone and maybe you >>> will figure out what is going on... >>> >>> Regarding why you can't just add Bio::LocatableSeq objects and have >>> add_seq just set the coordinates by itself, I investigated my long >>> forgotten code and just realized that the whole problem was that the >>> coordinates of a Bio::LocatableSeq object represent the location of >>> the object in the original sequence (i.e. unaligned read coordinates) >>> instead of its coordinates in the aligned consensus sequence. >>> Bio::LocatableSeq issues a warning whenever you try to set the object >>> start and end coordinates to the gapped consensus coordinates because >>> such coordinates lead to a length shorter than the actual read length: >>> >>> use Bio::LocatableSeq; >>> use Bio::SeqFeature::Collection; >>> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >>> =>"agggcACT-Gccc", -id=>"uga"); >>> my $sfc = Bio::SeqFeature::Collection->new(); >>> $sfc->add_features([ $ls ]); >>> print $sfc->feature_count,"\t",$ls->length."\n"; >>> >>> Additionally, Bio::LocatableSeq objects do not support the >>> primary_tag() method because they are just Bio::RangeI and not >>> Bio::SeqFeatureI objects. These two issues prevented me from using >>> Bio::LocatableSeq coordinates to represent gapped consensus >>> coordinates but the example code above suggests suppressing >>> Bio::LocatableSeq warnings and using the object class >>> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >>> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >>> the need for extra Bio::SeqFeature::Generic objects to store read >>> coordinates. >>> >>>> Since you said 'feel free to act', I have been faffing around here: >>>> http://github.com/dbolser/bioperl-live >>>> I'm not really sure if that is so useful, please advise. >>> >>> The comments I made above points to one area where you could have some >>> improvements in both memory usage and usability: drop the need for >>> additional Bio::SeqFeatureI objects to represent gapped consensus >>> coordinates. It would require you to check all Contig.pm methods for >>> the use of the "_aligned_coord:$readID" tags (I don't expect to see >>> any references to this outside Contig.pm) and change set_seq_coord to >>> a method that changes/sets the start and end values of the >>> Bio::LocatableSeq objects. >>> This might be a bit of work so just go for it if you want and have >>> time to experiment. >>> >>> Another detail: could you please replace references in Contig.pm and >>> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >>> not exists to the correct Bio::* classes? Somebody changed this to the >>> wrong names long ago... >>> >>>> Thanks again for help, >>> >>> Well these are my thoughts on the matter. Write again if you decide to >>> take this on and are unable to make progress. >>> Best, >>> Robson >>> >>>> Dan. >>>> >>>> >>>> P.S. >>>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>>> >>>> >>>> On 25 July 2010 15:42, Robson de Souza wrote: >>>>> Hi Dan, >>>>> >>>>> It is been a long time since I last loooked at this but, if I remember >>>>> correctly, the point is that Bio:: >>>>> >>>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>>> The following bug report boils down to this question: >>>>>> How should two sequence objects be compared for identity? Does the >>>>>> object override 'eq' or implement an 'identical' method? >>>>> >>>>> I think an 'identical' or 'equal' method would be the best alternative >>>>> since having a full method call would allow passing arguments like >>>>> '-mode => "complete"' to check all sequence features and annotations >>>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>>> id() is tracked most of the time (because of the internal hashes). >>>>> >>>>>> I found the following apparent bug in Contig.pm while executing the >>>>>> documented 'SYNOPSIS' code: >>>>> [snip] >>>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>>> sequence is added to the contig." >>>>> >>>>> In fact, it should not print warnings all the time.... >>>>> >>>>>> The offending line in that function seems to be: >>>>>> ?if( ... && >>>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>>> ? ? ? ? ?... >>>>>> ?} >>>>>> ?$self->add_seq($seq); >>>>>> which compares the *passed* sequence object to the sequence string for >>>>>> the *stored* sequence object of the same name. This comparison is >>>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>>> spews warnings if called after add_seq. >>>>> >>>>> Not the sequence string, but the objects themselves, i.e. the string >>>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>>> based version of identical() :) >>>>> >>>>>> Out of curiosity, how come I can't just say: >>>>>> my $ls = Bio::LocatableSeq-> >>>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>>> ? ? ? -id ? ? ? => 'r1', >>>>>> ? ? ? -alphabet => 'dna' >>>>>> ? ? ? -start ? ?=> 3, >>>>>> ? ? ? -end ? ? ?=> 8, >>>>>> ? ? ? -strand ? => 1 >>>>>> ? ? ); >>>>>> $c->add_seq( $ls ); >>>>> >>>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>>> would be nice to change it... you just need to create a >>>>> Bio::SeqFeature::Generic when >>>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>>> >>>>> Best, >>>>> Robson >>>>> >>>>>> I hope the above report can be of some use. >>>>>> >>>>>> Sincerely, >>>>>> Dan. >>>>>> _______________________________________________ >>>>>> 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 Jul 27 09:45:25 2010 From: scott at scottcain.net (Scott Cain) Date: Tue, 27 Jul 2010 09:45:25 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, You might find the deobfuscator helpful: http://bioperl.org/cgi-bin/deob_interface.cgi Scott On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: > On 26 July 2010 16:35, Scott Cain wrote: >> Hi Dan, >> >> I think there are probably several BioPerl classes that implement >> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >> for? > > A way to find what implements what... something like javadoc for bp. > > Really I'm looking for a nice 'ontology' of SeqFeatures. > > I was thinking that Contig.pm should implement Bio::SeqFeatureI. > > >> Scott >> >> >> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>> Which objects implement SeqFeatureI, and how should I find that info? >>> >>> Sorry for the gratuitous noobs. >>> >>> Cheers, >>> Dan. >>> _______________________________________________ >>> 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 >> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 Ontario Institute for Cancer Research From twaddlac at gmail.com Tue Jul 27 10:10:30 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:10:30 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: Hello, I am curious as to how I am supposed to use SeqIO::fastq to read in a fastq file and then obtain the nucleotide sequence from that. I noticed that SeqIO::fastq returns a Seq::Quality object but I haven't seen a method within that module that returns the nucleotide sequence. Please, let me know if you have any suggestions! Thank you very much!! -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 10:16:27 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:16:27 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: Message-ID: <4C4EEA3B.6020803@gmail.com> Hi Alan, Another case for the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say $seqqual->seq to get the sequence as a string. Cheers. Roy. On 27/07/2010 15:10, Alan Twaddle wrote: > Hello, > > I am curious as to how I am supposed to use SeqIO::fastq to read > in a fastq file and then obtain the nucleotide sequence from that. I > noticed that SeqIO::fastq returns a Seq::Quality object but I haven't > seen a method within that module that returns the nucleotide sequence. > Please, let me know if you have any suggestions! > > Thank you very much!! > From cjfields at illinois.edu Tue Jul 27 10:34:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 09:34:54 -0500 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Jul 27, 2010, at 4:02 AM, Dan Bolser wrote: > On 26 July 2010 18:54, Robson de Souza wrote: >> On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >>> Thanks again Robson, >>> >>> One thing I was going to email the list about is a lack of tests for >>> ace.pm and phrap.pm ... because of missing libs I'm not running the >>> sam or the maq tests, so any changes that I'm making to Contig.pm / >>> Scaffold.pm are not really being tested. >>> >>> Do you think anyone on the list (or you) would be able to generate a >>> few hundred tests to help me start modifying code with confidence? >> >> I hope so. I was reading Chris's presentation at BOSC and he mentioned >> that people are working on the support for the samtools so I believe >> somebody must have a dataset they could share. > > Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because > I don't have samtools installed. Also, (quick impression) method > coverage is limited (Contig.pm has a lot of methods!). > > I'll try to write some tests for ace.pm and phrap.pm. Tests are good! >> Never thought about it... but I can see that could be useful when >> contigs are part of higher level assemblies, like scaffolds or >> assembled chromosomes, but you could also achieve this by making >> Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any >> reason to prefer the Bio::SeqFeatureI interface? > > No. I don't have an overview of how the various objects relate to one > another, so any choice is more or less arbitrary. I'll try to write a > 'Sequence HOWTO'. > > > Thanks again for help, > Dan. Dan, The current HOWTOs (Beginner's, Feature/Annotation) should have this information, along with the BioPerl tutorial. chris From twaddlac at gmail.com Tue Jul 27 10:38:09 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:38:09 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EEA3B.6020803@gmail.com> References: <4C4EEA3B.6020803@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: > Hi Alan, > > Another case for the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi > > A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say > $seqqual->seq to get the sequence as a string. > > Cheers. > Roy. > > On 27/07/2010 15:10, Alan Twaddle wrote: >> >> Hello, >> >> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >> in a fastq file and then obtain the nucleotide sequence from that. I >> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >> seen a method within that module that returns the nucleotide sequence. >> Please, let me know if you have any suggestions! >> >> Thank you very much!! >> > > -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 10:50:21 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:50:21 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> Message-ID: <4C4EF22D.6050705@gmail.com> Hi Alan, It sounds like there's a problem with reading in your Fastq file. Are you using the latest BioPerl version? There have been many bug fixes to Bio::SeqIO::fastq over the last couple of years. If you are using an up-to-date BioPerl, please could you send an example Fastq entry which gives the error messages? Roy. On 27/07/2010 15:37, Alan Twaddle wrote: > Whenever I try to access the sequence I get the following error message: > > > --------------------- WARNING --------------------- > MSG: Seq/Qual descriptions don't match; using sequence description > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Fastq sequence/quality data length mismatch error > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + > --------------------------------------------------- > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Attempting to set the sequence to > [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] > which does not look healthy > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 > STACK: Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 > STACK: Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 > STACK: Bio::LocatableSeq::new > /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 > STACK: Bio::Seq::Meta::Array::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 > STACK: Bio::Seq::Quality::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 > STACK: Bio::Seq::SeqFactory::create > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 > STACK: Bio::SeqIO::fastq::next_seq > /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 > STACK: fastQParser.pl:12 > > > > On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> Another case for the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi >> >> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >> $seqqual->seq to get the sequence as a string. >> >> Cheers. >> Roy. >> >> On 27/07/2010 15:10, Alan Twaddle wrote: >>> >>> Hello, >>> >>> I am curious as to how I am supposed to use SeqIO::fastq to read >>> in a fastq file and then obtain the nucleotide sequence from that. I >>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>> seen a method within that module that returns the nucleotide sequence. >>> Please, let me know if you have any suggestions! >>> >>> Thank you very much!! >>> >> >> > > > From twaddlac at gmail.com Tue Jul 27 10:55:58 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:55:58 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EF22D.6050705@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: I'm not certain that I'm using the latest BioPerl, but I can check. In the mean time, I'll send you the example data! @FQ4HLCS02EO12Q region=2 tag=H +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII @FQ4HLCS02EO12T region=2 tag=B +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: > Hi Alan, > > It sounds like there's a problem with reading in your Fastq file. Are you > using the latest BioPerl version? There have been many bug fixes to > Bio::SeqIO::fastq over the last couple of years. If you are using an > up-to-date BioPerl, please could you send an example Fastq entry which gives > the error messages? > > Roy. > > On 27/07/2010 15:37, Alan Twaddle wrote: >> >> Whenever I try to access the sequence I get the following error message: >> >> >> --------------------- WARNING --------------------- >> MSG: Seq/Qual descriptions don't match; using sequence description >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: Fastq sequence/quality data length mismatch error >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >> --------------------------------------------------- >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Attempting to set the sequence to >> >> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >> which does not look healthy >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >> STACK: Bio::PrimarySeq::seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >> STACK: Bio::PrimarySeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >> STACK: Bio::LocatableSeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >> STACK: Bio::Seq::Meta::Array::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >> STACK: Bio::Seq::Quality::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >> STACK: Bio::Seq::SeqFactory::create >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >> STACK: Bio::SeqIO::fastq::next_seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >> STACK: fastQParser.pl:12 >> >> >> >> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >> ?wrote: >>> >>> Hi Alan, >>> >>> Another case for the deobfuscator: >>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>> $seqqual->seq to get the sequence as a string. >>> >>> Cheers. >>> Roy. >>> >>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>> >>>> Hello, >>>> >>>> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>> seen a method within that module that returns the nucleotide sequence. >>>> Please, let me know if you have any suggestions! >>>> >>>> Thank you very much!! >>>> >>> >>> >> >> >> > > -- Alan Twaddle, B.S. MUC class of 2010 From biopython at maubp.freeserve.co.uk Tue Jul 27 11:34:11 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Jul 2010 16:34:11 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > Hopefully this is just an email problem, but that doesn't look like a well formatted FASTQ record to me. Where is the "+" line separating the sequence and qualities? Maybe sending this single record as an attachment would work better (is that encouraged on this mailing list?). Peter From roy.chaudhuri at gmail.com Tue Jul 27 11:35:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 16:35:49 +0100 Subject: [Bioperl-l] Fwd: Re: How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: <4C4EFCD5.3030809@gmail.com> Forgot to cc the list: -------- Original Message -------- Subject: Re: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Date: Tue, 27 Jul 2010 16:03:53 +0100 From: Roy Chaudhuri To: Alan Twaddle That doesn't look like Fastq format as defined here: http://nar.oxfordjournals.org/cgi/content/full/gkp1137v1 http://en.wikipedia.org/wiki/FASTQ_format It shouldn't be difficult to write a script to parse it or convert to standard Fastq, though. > p.s. how do I find out what version of bioperl I'm using? http://www.bioperl.org/wiki/FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F On 27/07/2010 15:55, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > > > On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> It sounds like there's a problem with reading in your Fastq file. Are you >> using the latest BioPerl version? There have been many bug fixes to >> Bio::SeqIO::fastq over the last couple of years. If you are using an >> up-to-date BioPerl, please could you send an example Fastq entry which gives >> the error messages? >> >> Roy. >> >> On 27/07/2010 15:37, Alan Twaddle wrote: >>> >>> Whenever I try to access the sequence I get the following error message: >>> >>> >>> --------------------- WARNING --------------------- >>> MSG: Seq/Qual descriptions don't match; using sequence description >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: Fastq sequence/quality data length mismatch error >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >>> --------------------------------------------------- >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Attempting to set the sequence to >>> >>> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >>> which does not look healthy >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >>> STACK: Bio::PrimarySeq::seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >>> STACK: Bio::PrimarySeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >>> STACK: Bio::LocatableSeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >>> STACK: Bio::Seq::Meta::Array::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >>> STACK: Bio::Seq::Quality::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >>> STACK: Bio::Seq::SeqFactory::create >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >>> STACK: Bio::SeqIO::fastq::next_seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >>> STACK: fastQParser.pl:12 >>> >>> >>> >>> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >>> wrote: >>>> >>>> Hi Alan, >>>> >>>> Another case for the deobfuscator: >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>>> $seqqual->seq to get the sequence as a string. >>>> >>>> Cheers. >>>> Roy. >>>> >>>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>>> >>>>> Hello, >>>>> >>>>> I am curious as to how I am supposed to use SeqIO::fastq to read >>>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>>> seen a method within that module that returns the nucleotide sequence. >>>>> Please, let me know if you have any suggestions! >>>>> >>>>> Thank you very much!! >>>>> >>>> >>>> >>> >>> >>> >> >> > > > From cjfields at illinois.edu Tue Jul 27 11:57:43 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 10:57:43 -0500 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <41845A39-5F63-434A-92E6-86C4CA44C89B@illinois.edu> On Jul 27, 2010, at 10:34 AM, Peter wrote: > On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: >> I'm not certain that I'm using the latest BioPerl, but I can check. In >> the mean time, I'll send you the example data! >> >> @FQ4HLCS02EO12Q region=2 tag=H >> +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC >> +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII >> @FQ4HLCS02EO12T region=2 tag=B >> +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC >> +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 >> > > Hopefully this is just an email problem, but that doesn't look like a > well formatted > FASTQ record to me. Where is the "+" line separating the sequence and qualities? > > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). > > Peter As long as the attachment isn't many MB in size, I don't have a problem. Might get delayed by any spam filters though. chris From David.Messina at sbc.su.se Tue Jul 27 12:18:17 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 27 Jul 2010 10:18:17 -0600 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). Absolutely, please try resending as an attachment, Alan. Dave From david.breimann at gmail.com Sat Jul 24 02:47:43 2010 From: david.breimann at gmail.com (David B) Date: Fri, 23 Jul 2010 23:47:43 -0700 (PDT) Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date Message-ID: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Hi, I'm a bit confused about what is the best way to install and maintain the latest updates for bio perl (I'm working on linux). "Installing Bioperl for Unix" (http://www.bioperl.org/wiki/ Installing_Bioperl_for_Unix) suggests using Build.PL or CPAN, but then again I also know that bioperl is currently developed using github (although I know very little about github). 1. Is installing from github an alternative to Build.pL/CPAN options? 2. Does installing from github simply mean cloning than adding the path to PERL5LIB? That's it? 3. I want to use bp_genbank2gff3.pl for circular genomes and I was told I'd better use the developers release of bioperl because only it handles circular genomes correctly. Does it mean I need to clone ...- dev instead of -live and replace the path accordingly? Thanks, David From david.breimann at gmail.com Sat Jul 24 04:06:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sat, 24 Jul 2010 11:06:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl Message-ID: Hello, I'm trying to convert some genbank files downloaded from NCBI to GFF3 format but I keep getting error messages. My bioperl version (according to perl -MBio::Perl -le 'print Bio::Perl->VERSION;') is 1.0069 (I use github live branch). For example, I am trying to convert CP000249.gbk (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk): $ bp_genbank2gff3.pl CP000249.gbk # Input: CP000249.gbk # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia sp. CcI3, complete genome. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: must be scalar or CODE ref STACK: Error::throw STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/Root.pm:473 STACK: Bio::SeqFeature::Tools::TypeMapper::map_types /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 STACK: /usr/local/bin/bp_genbank2gff3.pl:411 ----------------------------------------------------------- Thanks, David From sc.ncrna at gmail.com Sun Jul 25 09:56:02 2010 From: sc.ncrna at gmail.com (ncRNA) Date: Sun, 25 Jul 2010 06:56:02 -0700 (PDT) Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination Message-ID: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Hi all, I am new to this forum and bioperl. I have a list of mouse genomic regions and would like to get the "corresponding" human genomic sequences, which can be seen from the comparative genomics tracks in the UCSC genome browser. Does anyone have any clue on how to realize this? Thanks in advance, ncRNA From twaddlac at gmail.com Tue Jul 27 12:36:43 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 12:36:43 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: Here's some of the data I would like to parse; the entire file was too big to send via email. Also, if there is some problem with the data, I would appreciate any scripting advice since I am unfortunately a noob :-/ Let me know what you think! Thank you all very much! On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >> Maybe sending this single record as an attachment would work better (is that >> encouraged on this mailing list?). > > Absolutely, please try resending as an attachment, Alan. > > > Dave > > -- Alan Twaddle, B.S. MUC class of 2010 -------------- next part -------------- A non-text attachment was scrubbed... Name: exampleData.fastq Type: application/octet-stream Size: 5510 bytes Desc: not available URL: From cjfields at illinois.edu Tue Jul 27 12:55:26 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 11:55:26 -0500 Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination In-Reply-To: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> References: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Message-ID: <2F614027-844E-43EA-8C01-D7C5C7EBF5E5@illinois.edu> Look at the ensembl API for this (I think compara in particular). chris On Jul 25, 2010, at 8:56 AM, ncRNA wrote: > Hi all, > > I am new to this forum and bioperl. I have a list of mouse genomic > regions and would like to get the "corresponding" human genomic > sequences, which can be seen from the comparative genomics tracks in > the UCSC genome browser. Does anyone have any clue on how to realize > this? > > Thanks in advance, > ncRNA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Tue Jul 27 13:14:48 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 18:14:48 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: <4C4F1408.3090707@gmail.com> Hi Alan, It looks like there wasn't any problem with the earlier e-mail, and that your file is not Fastq, but rather some unusual Fastq-like format - where did you get the file from? Here's a one-liner to convert your file into standard Fastq: perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < exampleData.fastq > standard.fastq I've assumed that your sequences and qualities are all single-line with a + prefix. Once you have a standard Fastq file you should be able to parse it with BioPerl. Roy. On 27/07/2010 17:36, Alan Twaddle wrote: > Here's some of the data I would like to parse; the entire file was too > big to send via email. Also, if there is some problem with the data, I > would appreciate any scripting advice since I am unfortunately a noob > :-/ > > Let me know what you think! > > Thank you all very much! > > On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >>> Maybe sending this single record as an attachment would work better (is that >>> encouraged on this mailing list?). >> >> Absolutely, please try resending as an attachment, Alan. >> >> >> Dave >> >> > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From twaddlac at gmail.com Tue Jul 27 14:57:16 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 14:57:16 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4F1408.3090707@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> <4C4F1408.3090707@gmail.com> Message-ID: Ahh thank you very much, everyone!!!! The data was from a GS-FLX Titanium sequencer but it was parsed out of a database into the format that was the "incorrect" fastq style. However, the script worked (though I'm not confident I understand what it just did) and I have successfully parsed the data out of it via BioPerl! Thanks again!! On Tue, Jul 27, 2010 at 1:14 PM, Roy Chaudhuri wrote: > Hi Alan, > > It looks like there wasn't any problem with the earlier e-mail, and that > your file is not Fastq, but rather some unusual Fastq-like format - where > did you get the file from? > > Here's a one-liner to convert your file into standard Fastq: > > perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < > exampleData.fastq > standard.fastq > > I've assumed that your sequences and qualities are all single-line with a + > prefix. > > Once you have a standard Fastq file you should be able to parse it with > BioPerl. > > Roy. > > On 27/07/2010 17:36, Alan Twaddle wrote: >> >> Here's some of the data I would like to parse; the entire file was too >> big to send via email. Also, if there is some problem with the data, I >> would appreciate any scripting advice since I am unfortunately a noob >> :-/ >> >> Let me know what you think! >> >> Thank you all very much! >> >> On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina >> ?wrote: >>>> >>>> Maybe sending this single record as an attachment would work better (is >>>> that >>>> encouraged on this mailing list?). >>> >>> Absolutely, please try resending as an attachment, Alan. >>> >>> >>> Dave >>> >>> >> >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Alan Twaddle, B.S. MUC class of 2010 From cjm at berkeleybop.org Tue Jul 27 18:14:00 2010 From: cjm at berkeleybop.org (Chris Mungall) Date: Tue, 27 Jul 2010 15:14:00 -0700 Subject: [Bioperl-l] bp_genbank2gff3.pl In-Reply-To: References: Message-ID: Hi David I can't replicate this, but I just pushed a change that gives more informative error messages on the 'circular' branch (same branch I pushed the unflattener temp fix for circular genomes) On Jul 24, 2010, at 1:06 AM, David Breimann wrote: > Hello, > > I'm trying to convert some genbank files downloaded from NCBI to GFF3 > format but I keep getting error messages. > > My bioperl version (according to perl -MBio::Perl -le 'print > Bio::Perl->VERSION;') is 1.0069 (I use github live branch). > > For example, I am trying to convert CP000249.gbk > (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk > ): > > $ bp_genbank2gff3.pl CP000249.gbk > # Input: CP000249.gbk > # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia > sp. CcI3, complete genome. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: must be scalar or CODE ref > STACK: Error::throw > STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/ > Root.pm:473 > STACK: Bio::SeqFeature::Tools::TypeMapper::map_types > /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 > STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 > STACK: /usr/local/bin/bp_genbank2gff3.pl:411 > ----------------------------------------------------------- > > Thanks, > David > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lairdm at sfu.ca Tue Jul 27 19:55:08 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 16:55:08 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ Message-ID: <4C4F71DC.7090503@sfu.ca> Good day, Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? Unfortunately the + sign in the name makes it a little hard to google. :) Thanks. From cjfields at illinois.edu Tue Jul 27 21:29:52 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 20:29:52 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4F71DC.7090503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> Message-ID: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > Good day, > > Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? > > Unfortunately the + sign in the name makes it a little hard to google. :) > > Thanks. Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: http://www.bioperl.org/wiki/HOWTO:BlastPlus chris From maj at fortinbras.us Wed Jul 28 00:51:03 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 28 Jul 2010 00:51:03 -0400 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <9BBF74930A5B477FACC15A4E72E98679@NewLife> >is not backward compatible with StandAloneBlast code, which is a feature, not a >bug ;> If that's not the nicest thing anyone's ever said.... ----- Original Message ----- From: "Chris Fields" To: "Matthew Laird" Cc: Sent: Tuesday, July 27, 2010 9:29 PM Subject: Re: [Bioperl-l] StandAloneBlast & BLAST+ > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the >> docs, and based on my quick testing the answer appears to be no, but does >> Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ > (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and > am trying to get our cluster switched over to it as well. It is not backward > compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get > the github version for this. There is also a bit of online documentation on > this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From lairdm at sfu.ca Wed Jul 28 01:14:05 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 22:14:05 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <4C4FBC9D.2020503@sfu.ca> Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... Thanks for the work guys, we couldn't do it without Bioperl at the core. On 10-07-27 06:29 PM, Chris Fields wrote: > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris From dan.bolser at gmail.com Wed Jul 28 05:59:39 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 10:59:39 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 27 July 2010 14:45, Scott Cain wrote: > Hi Dan, > > You might find the deobfuscator helpful: > > ?http://bioperl.org/cgi-bin/deob_interface.cgi I've tried to use that, but I don't understand how to get it to list the objects that implement a certain interface. > Scott > > > On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: >> On 26 July 2010 16:35, Scott Cain wrote: >>> Hi Dan, >>> >>> I think there are probably several BioPerl classes that implement >>> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >>> for? >> >> A way to find what implements what... something like javadoc for bp. >> >> Really I'm looking for a nice 'ontology' of SeqFeatures. >> >> I was thinking that Contig.pm should implement Bio::SeqFeatureI. >> >> >>> Scott >>> >>> >>> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>>> Which objects implement SeqFeatureI, and how should I find that info? >>>> >>>> Sorry for the gratuitous noobs. >>>> >>>> Cheers, >>>> Dan. >>>> _______________________________________________ >>>> 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 >>> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net > GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 > Ontario Institute for Cancer Research > From dan.bolser at gmail.com Wed Jul 28 06:07:38 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 11:07:38 +0100 Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date In-Reply-To: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> References: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Message-ID: On 24 July 2010 07:47, David B wrote: > Hi, > 1. Is installing from github an alternative to Build.pL/CPAN options? Yes, see this page: http://www.bioperl.org/wiki/Using_Git > 2. Does installing from github simply mean cloning than adding the > path to PERL5LIB? That's it? You could do that, or you could apply 'the mantra': perl Build.PL ./Build test ./Build install Don't forget to complain about all failed tests to the appropriate maintainers. > 3. I want to use bp_genbank2gff3.pl for circular genomes and I was > told I'd better use the developers release of bioperl because only it > handles circular genomes correctly. Does it mean I need to clone ...- > dev instead of -live and replace the path accordingly? AFAICT, bioperl-live is "the developers release". Just don't install "bioperl-dead" ... that's really, really bad. > Thanks, > David > > _______________________________________________ > 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 Jul 28 08:56:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 07:56:41 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4FBC9D.2020503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> <4C4FBC9D.2020503@sfu.ca> Message-ID: <397C1B19-0924-4836-B56F-026779E50943@illinois.edu> I'll be working on a 1.6.2 release very soon (had a slight delay due to problems with circular seqs). But BioPerl-Run and others will also be released as well. On Jul 28, 2010, at 12:14 AM, Matthew Laird wrote: > Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? > > I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... > > Thanks for the work guys, we couldn't do it without Bioperl at the core. > > On 10-07-27 06:29 PM, Chris Fields wrote: >> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: >> >>> Good day, >>> >>> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >>> >>> Unfortunately the + sign in the name makes it a little hard to google. :) >>> >>> Thanks. >> >> Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> >> >> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: >> >> http://www.bioperl.org/wiki/HOWTO:BlastPlus >> >> chris From cjfields at illinois.edu Wed Jul 28 09:33:33 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 08:33:33 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > On 27 July 2010 14:45, Scott Cain wrote: >> Hi Dan, >> >> You might find the deobfuscator helpful: >> >> http://bioperl.org/cgi-bin/deob_interface.cgi > > I've tried to use that, but I don't understand how to get it to list > the objects that implement a certain interface. The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. chris From pengyu.ut at gmail.com Wed Jul 28 18:14:33 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 17:14:33 -0500 Subject: [Bioperl-l] Download sequence by genomic location Message-ID: I could download a sequence by location at genome browser. http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 I know that there are ways to get the sequence. But I don't see a way to get the sequence by location. Could anybody let me know if there is such a function in bioperl? http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database -- Regards, Peng From cjfields at illinois.edu Wed Jul 28 18:39:07 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:39:07 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Not for UCSC (IIRC they specifically requested that we not set this functionality up in case their servers were hit too often). I think Galaxy does this, though, and of course you have EntrezGene and the Ensembl API as alternatives. Might be worth re-checking with the UCSC folks to see what their take is on this now... chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 18:47:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:47:08 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Forgot completely, but this should be possible via Bio::DAS: http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm I have used it myself via GBrowse. chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 18:54:44 2010 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 28 Jul 2010 18:54:44 -0400 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: On Wed, Jul 28, 2010 at 6:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database Hi, Peng. You could use the DAS API at the UCSC browser: http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=1:1,1000 The DAS spec is here: http://www.biodas.org/documents/spec-1.53.html And the UCSC FAQ entry is here: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 You could also download the chromosome files from UCSC and then use a FASTA indexing module from bioperl to allow quick random access to the files. I know you are also an R user, so you could use the BSgenome package and the appropriate genome to do the same thing. Sean From pengyu.ut at gmail.com Wed Jul 28 23:40:14 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 22:40:14 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: I didn't see a document for Bio::Das in my bioperl, $ perldoc Bio::Das No documentation found for "Bio::Das". $ perldoc Bio::Das::SegmentI $ perldoc Bio::Das::FeatureTypeI I thought that maybe my bioperl installation is corrupted. Then I install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I install it by "cpan -f Bio::Das". I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the example. It seems that the there is still something missing. I guess there must be some problem with my bioperl installation. Shall I reinstall it? Is there an easy fix? $ ./main.pl Using password in unencrypted URI against RFC #2396 recommendation at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm line 331. Must have IO::Socket::SSL installed to use https: urls: Can't locate Net/SSLeay.pm in @INC (@INC contains: /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. BEGIN failed--compilation aborted at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. Compilation failed in require at (eval 41) line 3. at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm line 200 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new(5); # timeout of 5 sec my @response = $das->dsn('http://stein.cshl.org/perl/das', 'http://genome.cse.ucsc.edu/cgi-bin/das', 'http://user:pass at www.wormbase.org/db/das', 'https://euclid.well.ox.ac.uk/cgi-bin/das', ); for my $url (@response) { if ($url->is_success) { my @dsns = $url->results; print "$url:\t\n"; foreach (@dsns) { print "\t",$_->url,"\t",$_->description,"\n"; } } else { print "$url: ",$url->error,"\n"; } } On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: > Forgot completely, but this should be possible via Bio::DAS: > > http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm > > I have used it myself via GBrowse. > > chris > > On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > >> I could download a sequence by location at genome browser. >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >> >> I know that there are ways to get the sequence. But I don't see a way >> to get the sequence by location. Could anybody let me know if there is >> such a function in bioperl? >> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >> >> -- >> Regards, >> Peng >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Regards, Peng From cjfields at illinois.edu Thu Jul 29 00:46:56 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 23:46:56 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: It's not part of BioPerl, but is on CPAN: http://search.cpan.org/dist/Bio-Das/ You don't appear to be following the Bio::Das API. The following worked for me: #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new( -source => 'http://genome.cse.ucsc.edu/cgi-bin/das', -dsn => 'hg18', ); my $segment = $das->segment('1:1,100000'); for my $sf ($segment->features) { printf("%s(%s):%d-%d(%d)\n", $sf->display_name, $sf->primary_tag, $sf->start, $sf->end, $sf->strand); } chris On Jul 28, 2010, at 10:40 PM, Peng Yu wrote: > I didn't see a document for Bio::Das in my bioperl, > > $ perldoc Bio::Das > No documentation found for "Bio::Das". > $ perldoc Bio::Das::SegmentI > $ perldoc Bio::Das::FeatureTypeI > > I thought that maybe my bioperl installation is corrupted. Then I > install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I > install it by "cpan -f Bio::Das". > > I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the > example. It seems that the there is still something missing. I guess > there must be some problem with my bioperl installation. > > Shall I reinstall it? Is there an easy fix? > > $ ./main.pl > Using password in unencrypted URI against RFC #2396 recommendation at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm > line 331. > Must have IO::Socket::SSL installed to use https: urls: Can't locate > Net/SSLeay.pm in @INC (@INC contains: > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > BEGIN failed--compilation aborted at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > Compilation failed in require at (eval 41) line 3. > at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm > line 200 > > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::Das; > > my $das = Bio::Das->new(5); # timeout of 5 sec > my @response = $das->dsn('http://stein.cshl.org/perl/das', > 'http://genome.cse.ucsc.edu/cgi-bin/das', > 'http://user:pass at www.wormbase.org/db/das', > 'https://euclid.well.ox.ac.uk/cgi-bin/das', > ); > > for my $url (@response) { > if ($url->is_success) { > my @dsns = $url->results; > print "$url:\t\n"; > foreach (@dsns) { > print "\t",$_->url,"\t",$_->description,"\n"; > } > } else { > print "$url: ",$url->error,"\n"; > } > } > > > On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: >> Forgot completely, but this should be possible via Bio::DAS: >> >> http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm >> >> I have used it myself via GBrowse. >> >> chris >> >> On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: >> >>> I could download a sequence by location at genome browser. >>> >>> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >>> >>> I know that there are ways to get the sequence. But I don't see a way >>> to get the sequence by location. Could anybody let me know if there is >>> such a function in bioperl? >>> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >>> >>> -- >>> Regards, >>> Peng >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > > -- > Regards, > Peng > _______________________________________________ > 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 Thu Jul 29 04:08:46 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 09:08:46 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 28 July 2010 14:33, Chris Fields wrote: > On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > >> On 27 July 2010 14:45, Scott Cain wrote: >>> Hi Dan, >>> >>> You might find the deobfuscator helpful: >>> >>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >> >> I've tried to use that, but I don't understand how to get it to list >> the objects that implement a certain interface. > > The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. OK, so at least I'm not being totally dumb when I can't find this info easily... I'll see if I can script it and add the results to the wiki. > chris From cjfields at illinois.edu Thu Jul 29 09:15:11 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jul 2010 08:15:11 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > On 28 July 2010 14:33, Chris Fields wrote: >> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >> >>> On 27 July 2010 14:45, Scott Cain wrote: >>>> Hi Dan, >>>> >>>> You might find the deobfuscator helpful: >>>> >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> I've tried to use that, but I don't understand how to get it to list >>> the objects that implement a certain interface. >> >> The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. > > OK, so at least I'm not being totally dumb when I can't find this info > easily... I'll see if I can script it and add the results to the wiki. > > >> chris Or, better yet, add it to the /scripts or /examples directory for bioperl-live. Code on the wiki can tend to get lost unless it's in a very accessible place. chris From james-platt at hotmail.co.uk Thu Jul 29 10:18:13 2010 From: james-platt at hotmail.co.uk (James) Date: Thu, 29 Jul 2010 07:18:13 -0700 (PDT) Subject: [Bioperl-l] Newbie question installing on MacOSX Message-ID: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Sorry for the newbie question. I am having trouble installing Bioperl. I'm on MacOSX 10.5.8. I downloaded and installed fink: $ fink --version Package manager version: 0.27.13 Distribution version: 0.9.0 i386 I then downloaded Bioperl-1.6.1, I'm trying to install it from source, as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have Xcode installed etc. '# fink install bioperl-pmXXX' I try this: BioPerl-1.6.1 James$ fink install BioPerl-pm Information about 2521 packages read in 1 seconds. Failed: no package found for specification 'BioPerl-pm'! The version of perl I'm running is 5.8.8, I have tried 'fink install BioPerl588' but this doesn't work either. Thanks very much, James From awitney at sgul.ac.uk Thu Jul 29 11:06:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Thu, 29 Jul 2010 16:06:01 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <08188444-D800-43FD-B1BB-4E1B4332BB46@sgul.ac.uk> Hi James, You are mixing up your installation methods. Either install with fink, or download the source and install from there, not both. I would personally recommend installing it from source or better still install from cpan. Take a look here: http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_Build.PL http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN If you really want to use fink then take a look here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink It looks like the command for this is: fink install bioperl-pm588 but I don't use fink any more so I am not certain of how that works. adam On 29 Jul 2010, at 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 11:23:06 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:23:06 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <4C519CDA.8010008@gmail.com> Hi James, I don't know anything about Macs, but looking here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink shouldn't the command be "fink install bioperl-pm588"? Roy. On 29/07/2010 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 11:36:11 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:36:11 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> Message-ID: <4C519FEB.8050702@gmail.com> Please copy replies to the mailing list, that way others can respond. Try the command: perl -MBio::Seq -e '' If Bioperl is not installed you will get an error message starting "Can't locate Bio/Seq in @INC". If the command just exits silently then BioPerl is installed correctly. Roy. On 29/07/2010 16:29, James Platt wrote: > Hi, > > I tried that, sorry I wasn't clear in the first post. > > James$ fink install bioperl-pm588 > Information about 2521 packages read in 0 seconds. > Failed: no package found for specification 'bioperl-pm588'! > > I think I may have installed it through fink commander. how do i check > in unix that it is in fact installed? > > Thanks, > > James > > On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: > >> Hi James, >> >> I don't know anything about Macs, but looking here: >> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >> >> shouldn't the command be "fink install bioperl-pm588"? >> >> Roy. >> >> On 29/07/2010 15:18, James wrote: >>> Sorry for the newbie question. >>> >>> I am having trouble installing Bioperl. >>> >>> I'm on MacOSX 10.5.8. >>> >>> I downloaded and installed fink: >>> >>> $ fink --version >>> Package manager version: 0.27.13 >>> Distribution version: 0.9.0 i386 >>> >>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>> source, >>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>> Xcode installed etc. >>> >>> '# fink install bioperl-pmXXX' >>> >>> I try this: >>> >>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>> >>> Information about 2521 packages read in 1 seconds. >>> Failed: no package found for specification 'BioPerl-pm'! >>> >>> >>> The version of perl I'm running is 5.8.8, I have tried 'fink install >>> BioPerl588' but this doesn't work either. >>> >>> Thanks very much, >>> >>> James >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From james-platt at hotmail.co.uk Thu Jul 29 12:11:48 2010 From: james-platt at hotmail.co.uk (James Platt) Date: Thu, 29 Jul 2010 17:11:48 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <4C519FEB.8050702@gmail.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> <4C519FEB.8050702@gmail.com> Message-ID: when I'm in the directory it exits silently. When I'm not... James$ perl -MBio::Seq -e '' Can't locate Bio/Seq.pm in @INC (@INC contains: /sw/lib/perl5/darwin- thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/ Updates/5.8.8 /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 .). BEGIN failed--compilation aborted. I guess I need to try install it again. J On 29 Jul 2010, at 16:36, Roy Chaudhuri wrote: > Please copy replies to the mailing list, that way others can respond. > > Try the command: > perl -MBio::Seq -e '' > > If Bioperl is not installed you will get an error message starting > "Can't locate Bio/Seq in @INC". If the command just exits silently > then BioPerl is installed correctly. > > Roy. > > On 29/07/2010 16:29, James Platt wrote: >> Hi, >> >> I tried that, sorry I wasn't clear in the first post. >> >> James$ fink install bioperl-pm588 >> Information about 2521 packages read in 0 seconds. >> Failed: no package found for specification 'bioperl-pm588'! >> >> I think I may have installed it through fink commander. how do i >> check >> in unix that it is in fact installed? >> >> Thanks, >> >> James >> >> On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: >> >>> Hi James, >>> >>> I don't know anything about Macs, but looking here: >>> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >>> >>> shouldn't the command be "fink install bioperl-pm588"? >>> >>> Roy. >>> >>> On 29/07/2010 15:18, James wrote: >>>> Sorry for the newbie question. >>>> >>>> I am having trouble installing Bioperl. >>>> >>>> I'm on MacOSX 10.5.8. >>>> >>>> I downloaded and installed fink: >>>> >>>> $ fink --version >>>> Package manager version: 0.27.13 >>>> Distribution version: 0.9.0 i386 >>>> >>>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>>> source, >>>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>>> Xcode installed etc. >>>> >>>> '# fink install bioperl-pmXXX' >>>> >>>> I try this: >>>> >>>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>>> >>>> Information about 2521 packages read in 1 seconds. >>>> Failed: no package found for specification 'BioPerl-pm'! >>>> >>>> >>>> The version of perl I'm running is 5.8.8, I have tried 'fink >>>> install >>>> BioPerl588' but this doesn't work either. >>>> >>>> Thanks very much, >>>> >>>> James >>>> >>>> _______________________________________________ >>>> 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 Thu Jul 29 14:17:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 19:17:42 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 29 July 2010 14:15, Chris Fields wrote: > On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > >> On 28 July 2010 14:33, Chris Fields wrote: >>> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >>> >>>> On 27 July 2010 14:45, Scott Cain wrote: >>>>> Hi Dan, >>>>> >>>>> You might find the deobfuscator helpful: >>>>> >>>>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> I've tried to use that, but I don't understand how to get it to list >>>> the objects that implement a certain interface. >>> >>> The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. >> >> OK, so at least I'm not being totally dumb when I can't find this info >> easily... I'll see if I can script it and add the results to the wiki. >> >> >>> chris > > Or, better yet, add it to the /scripts or /examples directory for bioperl-live. ?Code on the wiki can tend to get lost unless it's in a very accessible place. I meant I'd add the results to the wiki. Nice idea to add the code to the distro. > chris From frederic.romagne at gmail.com Fri Jul 30 00:59:35 2010 From: frederic.romagne at gmail.com (=?ISO-8859-1?Q?Fr=E9d=E9ric_Romagn=E9?=) Date: Fri, 30 Jul 2010 14:59:35 +1000 Subject: [Bioperl-l] phyloxml and element order Message-ID: Hi, I'm using bioperl to create phyloxml trees, after few tentatives, i got my tree with all the element/attributes i want but when I write the tree, element are not written following the order specified in the XSD Schema. For example, i got : Loxosceles intermedia Araneomorphae Sicariidae 969 HAAERADSRKPIWDIAHMVNDLELVD Araneomorphae Sicariidae The program forester complains that should be written before the element. According to http://phyloxml.wordpress.com/2009/11/25/order-of-elements-in-phyloxml this is what bioperl is supposed to do. All my element/attributes are set before writing the tree using 'add_Annotation', 'add_tag_value' and 'sequence' methods from a Bio::Tree::AnnotatableNode object, so i think the error comes from the write_tree method. Any help would be appreciated. Thank you, Fred From com505 at york.ac.uk Fri Jul 30 05:37:11 2010 From: com505 at york.ac.uk (Carrie O'Malley) Date: Fri, 30 Jul 2010 10:37:11 +0100 Subject: [Bioperl-l] installing bioperl Message-ID: Hi there I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. I am not able to complete the installation as every time I get: Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have tried using both methods to install into a local folder and get the same thing !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/home/users/carrieomalley/bin' mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( Many thanks in advance Carrie Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: Data::Stag is not installed (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) CPAN: Storable loaded ok (v2.18) Going to read /Users/carrieomalley/.cpan/Metadata Database was generated on Sat, 10 Jul 2010 11:27:04 GMT Running install for module 'Data::Stag' 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok x Data-Stag-0.11/ x Data-Stag-0.11/c-ext/ x Data-Stag-0.11/c-ext/README.c-ext x Data-Stag-0.11/c-ext/staglib.c x Data-Stag-0.11/c-ext/staglib.h x Data-Stag-0.11/Changes x Data-Stag-0.11/Data/ x Data-Stag-0.11/Data/Stag/ x Data-Stag-0.11/Data/Stag/Arr2HTML.pm x Data-Stag-0.11/Data/Stag/Base.pm x Data-Stag-0.11/Data/Stag/BaseGenerator.pm x Data-Stag-0.11/Data/Stag/BaseHandler.pm x Data-Stag-0.11/Data/Stag/ChainHandler.pm x Data-Stag-0.11/Data/Stag/DTDWriter.pm x Data-Stag-0.11/Data/Stag/GraphHandler.pm x Data-Stag-0.11/Data/Stag/HashDB.pm x Data-Stag-0.11/Data/Stag/IndentParser.pm x Data-Stag-0.11/Data/Stag/IndentWriter.pm x Data-Stag-0.11/Data/Stag/ITextParser.pm x Data-Stag-0.11/Data/Stag/ITextWriter.pm x Data-Stag-0.11/Data/Stag/null.pm x Data-Stag-0.11/Data/Stag/PerlWriter.pm x Data-Stag-0.11/Data/Stag/PodParser.pm x Data-Stag-0.11/Data/Stag/SAX2Stag.pm x Data-Stag-0.11/Data/Stag/Simple.pm x Data-Stag-0.11/Data/Stag/StagDB.pm x Data-Stag-0.11/Data/Stag/StagI.pm x Data-Stag-0.11/Data/Stag/StagImpl.pm x Data-Stag-0.11/Data/Stag/SxprParser.pm x Data-Stag-0.11/Data/Stag/SxprWriter.pm x Data-Stag-0.11/Data/Stag/Util.pm x Data-Stag-0.11/Data/Stag/Writer.pm x Data-Stag-0.11/Data/Stag/XMLParser.pm x Data-Stag-0.11/Data/Stag/XMLWriter.pm x Data-Stag-0.11/Data/Stag/XSLHandler.pm x Data-Stag-0.11/Data/Stag/XSLTHandler.pm x Data-Stag-0.11/Data/Stag.pm x Data-Stag-0.11/dev/ x Data-Stag-0.11/dev/create-manifest.sh x Data-Stag-0.11/dev/data-stag.spec x Data-Stag-0.11/dev/mkspec.pl x Data-Stag-0.11/elisp/ x Data-Stag-0.11/elisp/itext-mode.el x Data-Stag-0.11/homepage/ x Data-Stag-0.11/homepage/archBIG.png x Data-Stag-0.11/homepage/dbstag-tutorial.sgml x Data-Stag-0.11/homepage/images/ x Data-Stag-0.11/homepage/images/k-schema-diagram.png x Data-Stag-0.11/homepage/images/rr-schema-diagram.png x Data-Stag-0.11/homepage/index.html x Data-Stag-0.11/homepage/makefile x Data-Stag-0.11/homepage/mk.sh x Data-Stag-0.11/homepage/mkpodhtml.pl x Data-Stag-0.11/homepage/mkscriptdoc.pl x Data-Stag-0.11/homepage/script-docs/ x Data-Stag-0.11/homepage/script-docs/selectall_html.html x Data-Stag-0.11/homepage/script-docs/selectall_xml.html x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html x Data-Stag-0.11/homepage/script-docs/stag-db.html x Data-Stag-0.11/homepage/script-docs/stag-diff.html x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html x Data-Stag-0.11/homepage/script-docs/stag-elcount.html x Data-Stag-0.11/homepage/script-docs/stag-eval.html x Data-Stag-0.11/homepage/script-docs/stag-filter.html x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html x Data-Stag-0.11/homepage/script-docs/stag-flatten.html x Data-Stag-0.11/homepage/script-docs/stag-grep.html x Data-Stag-0.11/homepage/script-docs/stag-handle.html x Data-Stag-0.11/homepage/script-docs/stag-ir.html x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html x Data-Stag-0.11/homepage/script-docs/stag-join.html x Data-Stag-0.11/homepage/script-docs/stag-merge.html x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html x Data-Stag-0.11/homepage/script-docs/stag-parse.html x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html x Data-Stag-0.11/homepage/script-docs/stag-query.html x Data-Stag-0.11/homepage/script-docs/stag-show-template.html x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html x Data-Stag-0.11/homepage/script-docs/stag-splitter.html x Data-Stag-0.11/homepage/script-docs/stag-storenode.html x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html x Data-Stag-0.11/homepage/script-docs/stag-view.html x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html x Data-Stag-0.11/homepage/script-list.html x Data-Stag-0.11/homepage/stag-db-tutorial.html x Data-Stag-0.11/homepage/stag-poster.html x Data-Stag-0.11/INSTALL x Data-Stag-0.11/Makefile.PL x Data-Stag-0.11/MANIFEST x Data-Stag-0.11/META.yml x Data-Stag-0.11/README x Data-Stag-0.11/scripts/ x Data-Stag-0.11/scripts/stag-autoschema.pl x Data-Stag-0.11/scripts/stag-db.pl x Data-Stag-0.11/scripts/stag-diff.pl x Data-Stag-0.11/scripts/stag-drawtree.pl x Data-Stag-0.11/scripts/stag-elcount.pl x Data-Stag-0.11/scripts/stag-eval.pl x Data-Stag-0.11/scripts/stag-filter.pl x Data-Stag-0.11/scripts/stag-findsubtree.pl x Data-Stag-0.11/scripts/stag-flatten.pl x Data-Stag-0.11/scripts/stag-grep.pl x Data-Stag-0.11/scripts/stag-handle.pl x Data-Stag-0.11/scripts/stag-itext2simple.pl x Data-Stag-0.11/scripts/stag-itext2sxpr.pl x Data-Stag-0.11/scripts/stag-itext2xml.pl x Data-Stag-0.11/scripts/stag-join.pl x Data-Stag-0.11/scripts/stag-merge.pl x Data-Stag-0.11/scripts/stag-mogrify.pl x Data-Stag-0.11/scripts/stag-parse.pl x Data-Stag-0.11/scripts/stag-query.pl x Data-Stag-0.11/scripts/stag-splitter.pl x Data-Stag-0.11/scripts/stag-view.pl x Data-Stag-0.11/scripts/stag-xml2itext.pl x Data-Stag-0.11/scripts/stag-xmlsplit.pl x Data-Stag-0.11/t/ x Data-Stag-0.11/t/animal.x x Data-Stag-0.11/t/autoschema.t x Data-Stag-0.11/t/barfly.x x Data-Stag-0.11/t/bio.x x Data-Stag-0.11/t/chainhandler.t x Data-Stag-0.11/t/collapse.x x Data-Stag-0.11/t/data/ x Data-Stag-0.11/t/data/attrs.xml x Data-Stag-0.11/t/data/bf.txt x Data-Stag-0.11/t/data/eco.el x Data-Stag-0.11/t/data/eco.itext x Data-Stag-0.11/t/data/homol.itext x Data-Stag-0.11/t/data/persons.el x Data-Stag-0.11/t/db.t x Data-Stag-0.11/t/emptytag.t x Data-Stag-0.11/t/get.t x Data-Stag-0.11/t/graph.x x Data-Stag-0.11/t/handlers.t x Data-Stag-0.11/t/handlers2.t x Data-Stag-0.11/t/handlers2.x x Data-Stag-0.11/t/hashdb.t x Data-Stag-0.11/t/hashdb.x x Data-Stag-0.11/t/homol.t x Data-Stag-0.11/t/lisp.x x Data-Stag-0.11/t/parsestr.t x Data-Stag-0.11/t/path.x x Data-Stag-0.11/t/path2.x x Data-Stag-0.11/t/qmatch.t x Data-Stag-0.11/t/roundtrip-attrs.t x Data-Stag-0.11/t/set-attrs.t x Data-Stag-0.11/t/set.t x Data-Stag-0.11/t/sxpr.t x Data-Stag-0.11/t/unhash.t x Data-Stag-0.11/t/unset.t x Data-Stag-0.11/t/write.t x Data-Stag-0.11/t/xml1.t x Data-Stag-0.11/t/xml2.t CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz External Module XML::LibXSLT, XSLT, is not installed on this computer. Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations External Module XML::Parser::PerlSAX, SAX Handler, is not installed on this computer. Data::Stag::XMLParser in Data::Stag needs it for parsing XML External Module GD, Graphical Drawing Toolkit, is not installed on this computer. stag-drawtree.pl in Data::Stag needs it for drawing trees External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer. Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs External Module Tk, Tk, is not installed on this computer. stag-view.pl in Data::Stag needs it for tree viewer Information: There are some external packages and perl modules, listed above, which stag uses. This only effects the functionality which is listed above: the rest of stag will work fine, which includes nearly all of the core functionality. Enjoy the rest of stag, which you can use after going 'make install' Checking if your kit is complete... Looks good Writing Makefile for Data Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm cp Data/Stag.pm blib/lib/Data/Stag.pm cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm cp scripts/stag-view.pl blib/script/stag-view.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl cp scripts/stag-grep.pl blib/script/stag-grep.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl cp scripts/stag-merge.pl blib/script/stag-merge.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl cp scripts/stag-parse.pl blib/script/stag-parse.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl cp scripts/stag-join.pl blib/script/stag-join.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl cp scripts/stag-db.pl blib/script/stag-db.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl cp scripts/stag-filter.pl blib/script/stag-filter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl cp scripts/stag-handle.pl blib/script/stag-handle.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl cp scripts/stag-query.pl blib/script/stag-query.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl cp scripts/stag-flatten.pl blib/script/stag-flatten.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl cp scripts/stag-splitter.pl blib/script/stag-splitter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl cp scripts/stag-diff.pl blib/script/stag-diff.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl Manifying blib/man1/stag-view.pl.1 Manifying blib/man1/stag-mogrify.pl.1 Manifying blib/man1/stag-grep.pl.1 Manifying blib/man1/stag-handle.pl.1 Manifying blib/man1/stag-drawtree.pl.1 Manifying blib/man1/stag-query.pl.1 Manifying blib/man1/stag-merge.pl.1 Manifying blib/man1/stag-parse.pl.1 Manifying blib/man1/stag-findsubtree.pl.1 Manifying blib/man1/stag-join.pl.1 Manifying blib/man1/stag-autoschema.pl.1 Manifying blib/man1/stag-db.pl.1 Manifying blib/man1/stag-flatten.pl.1 Manifying blib/man1/stag-splitter.pl.1 Manifying blib/man1/stag-diff.pl.1 Manifying blib/man1/stag-filter.pl.1 Manifying blib/man3/Data::Stag::StagDB.3pm Manifying blib/man3/Data::Stag::SxprWriter.3pm Manifying blib/man3/Data::Stag.3pm Manifying blib/man3/Data::Stag::ChainHandler.3pm Manifying blib/man3/Data::Stag::IndentParser.3pm Manifying blib/man3/Data::Stag::Simple.3pm Manifying blib/man3/Data::Stag::SAX2Stag.3pm Manifying blib/man3/Data::Stag::Arr2HTML.3pm Manifying blib/man3/Data::Stag::XSLHandler.3pm Manifying blib/man3/Data::Stag::PerlWriter.3pm Manifying blib/man3/Data::Stag::XSLTHandler.3pm Manifying blib/man3/Data::Stag::DTDWriter.3pm Manifying blib/man3/Data::Stag::Writer.3pm Manifying blib/man3/Data::Stag::XMLWriter.3pm Manifying blib/man3/Data::Stag::GraphHandler.3pm Manifying blib/man3/Data::Stag::XMLParser.3pm Manifying blib/man3/Data::Stag::StagImpl.3pm Manifying blib/man3/Data::Stag::PodParser.3pm Manifying blib/man3/Data::Stag::BaseGenerator.3pm Manifying blib/man3/Data::Stag::IndentWriter.3pm Manifying blib/man3/Data::Stag::HashDB.3pm Manifying blib/man3/Data::Stag::null.3pm Manifying blib/man3/Data::Stag::ITextParser.3pm Manifying blib/man3/Data::Stag::BaseHandler.3pm Manifying blib/man3/Data::Stag::ITextWriter.3pm Manifying blib/man3/Data::Stag::SxprParser.3pm CMUNGALL/Data-Stag-0.11.tar.gz make -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/autoschema.........ok t/chainhandler.......ok t/db.................ok t/emptytag...........ok 3/3 skipped: various reasons t/get................ok t/handlers...........ok t/handlers2..........ok 1/9 skipped: various reasons t/hashdb.............ok t/homol..............ok t/parsestr...........ok 6/6 skipped: various reasons t/qmatch.............ok t/roundtrip-attrs....ok 5/5 skipped: various reasons t/set-attrs..........ok 3/3 skipped: various reasons t/set................ok t/sxpr...............ok t/unhash.............ok t/unset..............ok t/write..............ok t/xml1...............ok 7/7 skipped: various reasons t/xml2...............ok 4/4 skipped: various reasons All tests successful, 29 subtests skipped. Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) CMUNGALL/Data-Stag-0.11.tar.gz make test -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make install Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1 make: *** [pure_site_install] Error 13 CMUNGALL/Data-Stag-0.11.tar.gz make install -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state *** (back in Bioperl Build.PL) *** Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n - ERROR: You chose to install Data::Stag but it failed to install * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Spreadsheet::ParseExcel is not installed (wanted for parsing Excel files, used by Bio::SeqIO::excel) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite Graph is not installed (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) * Optional prerequisite SVG::Graph is not installed (wanted for creating SVG images, used by Bio::TreeIO::svggraph) * Optional prerequisite SOAP::Lite is not installed (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Convert::Binary::C is not installed (wanted for strider functionality, used by Bio::SeqIO::strider) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite XML::Twig is not installed (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) * Optional prerequisite Set::Scalar is not installed (wanted for proper operation, used by Bio::Tree::Compatible) * Optional prerequisite XML::Parser::PerlSAX is not installed (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite Clone is not installed (wanted for cloning objects, used by Bio::Tools::Primer3) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: BioDBGFF.................disabled * MySQL, Pg nor Oracle DBI drivers are installed BioDBSeqFeature_mysql....disabled - DBD::mysql is not installed Network..................enabled BioDBSeqFeature_BDB......enabled Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] n - will not run internet-requiring tests Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'BioPerl' version '1.006000' Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok 1/28 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- # Looks like you planned 28 tests but only ran 7. # Looks like your test died just after 7. t/AlignIO/AlignIO............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 8-28 Failed 21/28 tests, 25.00% okay t/AlignIO/arp................................ok 1/48 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- # Looks like you planned 48 tests but only ran 2. # Looks like your test died just after 2. t/AlignIO/arp................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-48 Failed 46/48 tests, 4.17% okay 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......................ok 1/159 # Failed test 'use Bio::Annotation::TagTree;' # at t/Annotation/Annotation.t line 20. # Tried to use 'Bio::Annotation::TagTree'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. # Compilation failed in require at (eval 37) line 2. # BEGIN failed--compilation aborted at (eval 37) line 2. t/Annotation/Annotation......................NOK 9/159 # Failed test 'default itext' # at t/Annotation/Annotation.t line 307. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' # Failed test 'itext' # at t/Annotation/Annotation.t line 315. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. # Looks like you planned 159 tests but only ran 119. # Looks like you failed 3 tests of 119 run. # Looks like your test died just after 119. t/Annotation/Annotation......................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 9, 117, 119-159 Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................ok 1/51 # Failed (TODO) test at t/Assembly/Assembly.t line 35. t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok 1/24 skipped: various reasons t/Biblio/References..........................ok t/Biblio/biofetch............................skipped all skipped: Network tests have not been requested t/Biblio/eutils..............................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/ClusterIO/ClusterIO........................ok 8/12 skipped: various reasons t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/ClusterIO/SequenceFamily.t:16 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. # Looks like you planned 19 tests but only ran 2. # Looks like your test died just after 2. t/ClusterIO/SequenceFamily...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-19 Failed 17/19 tests, 10.53% okay 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 11/279 skipped: various reasons t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 STACK: t/LocalDB/Flat.t:89 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. # Looks like you planned 24 tests but only ran 14. # Looks like your test died just after 14. t/LocalDB/Flat...............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-24 Failed 10/24 tests, 58.33% okay t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 STACK: t/LocalDB/Index.t:91 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. # Looks like you planned 64 tests but only ran 31. # Looks like your test died just after 31. t/LocalDB/Index..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 32-64 Failed 33/64 tests, 48.44% okay t/LocalDB/Registry...........................ok 9/14 skipped: various reasons t/LocalDB/SeqFeature.........................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok 19/267 skipped: various reasons 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 10/14 skipped: various reasons t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok 10/29 skipped: various reasons 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..................................ok t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok 4/46 skipped: various reasons t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................skipped all skipped: Network tests have not been requested t/RemoteDB/CUTG..............................ok 14/37 skipped: various reasons t/RemoteDB/DB................................skipped all skipped: Network tests have not been requested t/RemoteDB/EMBL..............................skipped all skipped: Network tests have not been requested t/RemoteDB/EUtilities........................skipped all skipped: Network tests have not been requested t/RemoteDB/HIV/HIV...........................ok 13/30 skipped: various reasons t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok 10/41 skipped: various reasons t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok 10/16 skipped: various reasons t/RemoteDB/SeqHound..........................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqRead_fail......................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqVersion........................ok 8/10 skipped: various reasons t/RemoteDB/Taxonomy..........................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................ok 1/18 # Failed (TODO) test at t/Restriction/IO.t line 31. t/Restriction/IO.............................ok 3/18 skipped: various reasons t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................ok 2/31 skipped: various reasons t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped all 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.............................ok 1/1093 # Failed (TODO) test at t/SearchIO/blast.t line 527. # '0.852' # > # '0.9' # Failed (TODO) test at t/SearchIO/blast.t line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................ok 1/289 # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................ok 1/298 # Failed (TODO) test at t/SearchIO/blastxml.t line 258. # got: undef # expected: '31984247' # Failed (TODO) test at t/SearchIO/blastxml.t line 259. # got: undef # expected: '88780' # Failed (TODO) test at t/SearchIO/blastxml.t line 260. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok 4/45 skipped: various reasons 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...........................ok 1/116 # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. # got: 'Bio::Location::Simple=HASH(0x100838ce8)' # expected: undef # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test at t/Seq/LocatableSeq.t 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 all 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 all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok 7/214 skipped: various reasons t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqIO/Handler.t:20 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. # Looks like you planned 550 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/Handler..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-550 Failed 549/550 tests, 0.18% okay t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped all 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..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped all skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ # Failed test 'use Bio::SeqIO::chaos;' # at t/SeqIO/chaos.t line 15. # Tried to use 'Bio::SeqIO::chaos'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. # Looks like you failed 1 test of 8. t/SeqIO/chaos................................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/8 tests, 87.50% okay t/SeqIO/chaosxml.............................skipped all skipped: The optional module Data::Stag (or dependencies thereof) was not installed t/SeqIO/ctf..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped all 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 all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................ok 1/17 # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 54. # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped all 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 all 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 all 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..................................ok 1/59 # Failed (TODO) test 'accuracies' # at t/SeqIO/scf.t line 78. # got: 'ARRAY(0x100ac5648)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ # Failed test 'use Bio::SeqIO::swiss;' # at t/SeqIO/swiss.t line 12. # Tried to use 'Bio::SeqIO::swiss'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. # Looks like you planned 240 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqIO/swiss................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-240 Failed 240/240 tests, 0.00% okay t/SeqIO/tab..................................ok t/SeqIO/table................................ok 112/450 skipped: various reasons t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped all 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 1/49Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqTools/GuessSeqFormat.t:62 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time t/SeqTools/GuessSeqFormat....................NOK 25/49 # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. # ' # at t/SeqTools/GuessSeqFormat.t line 71. # got: '0' # expected: '1' # Looks like you planned 49 tests but ran 1 extra. # Looks like you failed 1 test of 50 run. t/SeqTools/GuessSeqFormat....................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED tests 25, 50 Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok 5/21 skipped: various reasons t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped all 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 all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut..............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos.............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/Tools/Analysis/Protein/Scansite.t:23 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. # Looks like you planned 14 tests but only ran 4. # Looks like your test died just after 4. t/Tools/Analysis/Protein/Scansite............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-14 Failed 10/14 tests, 28.57% okay t/Tools/Analysis/Protein/Sopma...............ok 12/16 skipped: various reasons 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 all 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......................skipped all skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast..................ok 12/45 skipped: various reasons 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 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 all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok 2/74 skipped: various reasons t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................ok t/Tree/TreeIO/svggraph.......................ok 3/4 skipped: various reasons 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 15/26 skipped: various reasons Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/AlignIO/AlignIO.t 255 65280 28 42 8-28 t/AlignIO/arp.t 255 65280 48 92 3-48 t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 t/LocalDB/Flat.t 255 65280 24 20 15-24 t/LocalDB/Index.t 255 65280 64 66 32-64 t/SeqIO/Handler.t 255 65280 550 1098 2-550 t/SeqIO/chaos.t 1 256 8 1 1 t/SeqIO/swiss.t 255 65280 240 479 1-240 t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 57 tests and 313 subtests skipped. Failed 11/318 test scripts. 970/17228 subtests failed. Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) Failed 11/318 test programs. 970/17228 subtests failed. Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 From robfsouza at gmail.com Fri Jul 30 09:54:08 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 30 Jul 2010 09:54:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Did you try, as root, ./Build.pl --install_base /opt/local ? Also, check the INSTALL file at the root of the bioperl distribution. Robson On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > ?I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > ?- ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > ?is not installed on this computer. > ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > ?is not installed on this computer. > ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > ?is not installed on this computer. > ?stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > ?is not installed on this computer. > ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > ?is not installed on this computer. > ?stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > ? There are some external packages and perl modules, listed above, which > ? stag uses. This only effects the functionality which is listed above: > ? the rest of stag will work fine, which includes nearly all of the > ? core functionality. > > ? Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > ? ? ? ?3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > ? ? ? ?1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > ? ? ? ?6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > ? ? ? ?5/5 skipped: various reasons > t/set-attrs..........ok > ? ? ? ?3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > ? ? ? ?7/7 skipped: various reasons > t/xml2...............ok > ? ? ? ?4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at -e line 1 > make: *** [pure_site_install] Error 13 > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make install ?-- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > ?- ERROR: You chose to install Data::Stag but it failed to install > ?* Optional prerequisite Ace is not installed > ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > ?* Optional prerequisite Spreadsheet::ParseExcel is not installed > ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) > ?* Optional prerequisite Math::Random is not installed > ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > ?* Optional prerequisite Graph is not installed > ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > ?* Optional prerequisite SVG::Graph is not installed > ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > ?* Optional prerequisite SOAP::Lite is not installed > ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed > ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > ?* Optional prerequisite GraphViz is not installed > ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > ?* Optional prerequisite Array::Compare is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite Convert::Binary::C is not installed > ? (wanted for strider functionality, used by Bio::SeqIO::strider) > ?* Optional prerequisite Algorithm::Munkres is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite XML::Twig is not installed > ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > ?* Optional prerequisite Set::Scalar is not installed > ? (wanted for proper operation, used by Bio::Tree::Compatible) > ?* Optional prerequisite XML::Parser::PerlSAX is not installed > ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > ?* Optional prerequisite XML::SAX::Writer is not installed > ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) > ?* Optional prerequisite Clone is not installed > ? (wanted for cloning objects, used by Bio::Tools::Primer3) > ?* Optional prerequisite XML::DOM::XPath is not installed > ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > ?* Optional prerequisite PostScript::TextBlock is not installed > ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > ?BioDBGFF.................disabled > ? ?* MySQL, Pg nor Oracle DBI drivers are installed > ?BioDBSeqFeature_mysql....disabled > ? ?- DBD::mysql is not installed > ?Network..................enabled > ?BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > ?- will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > ?- will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > ? ? ? ?Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > ? ? ? ?Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # ? Failed test 'use Bio::Annotation::TagTree;' > # ? at t/Annotation/Annotation.t line 20. > # ? ? Tried to use 'Bio::Annotation::TagTree'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # ? Failed test 'default itext' > # ? at t/Annotation/Annotation.t line 307. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > > # ? Failed test 'itext' > # ? at t/Annotation/Annotation.t line 315. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > ? ? ? ?1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > ? ? ? ?8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > ? ? ? ?Failed 17/19 tests, 10.53% okay > 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 > ? ? ? ?11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > ? ? ? ?Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > ? ? ? ?Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > ? ? ? ?9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > ? ? ? ?19/267 skipped: various reasons > 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 > ? ? ? ?10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > ? ? ? ?10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > ? ? ? ?4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > ? ? ? ?14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > ? ? ? ?13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > ? ? ? ?10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > ? ? ? ?10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > ? ? ? ?8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # ? Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > ? ? ? ?3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > ? ? ? ?2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > ? ? ? ?all 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.............................ok 1/1093 > # ? Failed (TODO) test at t/SearchIO/blast.t line 527. > # ? ? '0.852' > # ? ? ? ? > > # ? ? '0.9' > > # ? Failed (TODO) test at t/SearchIO/blast.t line 528. > # ? ? '1.599' > # ? ? ? ? <= > # ? ? '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # ? ? ? ? ?got: '0.946' > # ? ? expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # ? ? ? ? ?got: undef > # ? ? expected: '31984247' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # ? ? ? ? ?got: undef > # ? ? expected: '88780' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # ? ? ? ? ?got: undef > # ? ? expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > ? ? ? ?4/45 skipped: various reasons > 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...........................ok 1/116 > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # ? ? expected: undef > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # ? ? ? ? ?got: '\-\.=~' > # ? ? expected: '-\?' > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > ? ? ? ?7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > ? ? ? ?Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > ? ? ? ?all 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..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # ? Failed test 'use Bio::SeqIO::chaos;' > # ? at t/SeqIO/chaos.t line 15. > # ? ? Tried to use 'Bio::SeqIO::chaos'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > ? ? ? ?Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # ? Failed (TODO) test 'primary_id' > # ? at t/SeqIO/gcg.t line 54. > # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # ? ? expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > ? ? ? ?all 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 > ? ? ? ?all 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 > ? ? ? ?all 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..................................ok 1/59 > # ? Failed (TODO) test 'accuracies' > # ? at t/SeqIO/scf.t line 78. > # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' > # ? ? expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # ? Failed test 'use Bio::SeqIO::swiss;' > # ? at t/SeqIO/swiss.t line 12. > # ? ? Tried to use 'Bio::SeqIO::swiss'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > ? ? ? ?Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > ? ? ? ?112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # ? at t/SeqTools/GuessSeqFormat.t line 71. > # ? ? ? ? ?got: '0' > # ? ? expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > ? ? ? ?5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > ? ? ? ?Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > ? ? ? ?12/16 skipped: various reasons > 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 > ? ? ? ?all 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......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > ? ? ? ?12/45 skipped: various reasons > 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 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 > ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > ? ? ? ?2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > ? ? ? ?3/4 skipped: various reasons > 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 > ? ? ? ?15/26 skipped: various reasons > Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 > t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 > t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 > t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 > t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 > t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 > t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 > t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 > t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 > t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 > t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > 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 Fri Jul 30 11:26:12 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Fri, 30 Jul 2010 16:26:12 +0100 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: <70A35EB0-D004-4B7A-A239-D9EA7F9EA206@sgul.ac.uk> It looks like it is trying to install and failing because of lack of permissions. I would recommend you try the cpan route like this: perl -MCPAN -e shell then from the cpan prompt, set a few things up (only need to do this once): cpan> o conf make_install_make_command 'sudo make' cpan> o conf mbuild_install_build_command 'sudo ./Build' cpan> o conf commit cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz .... and keep an eye on it... it will ask for a password early on to allow it to install into the right directories. Or you if you want to retry your current method you could do this sudo perl ./Build.pl HTH adam On 30 Jul 2010, at 10:37, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > - ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > is not installed on this computer. > Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > is not installed on this computer. > Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > is not installed on this computer. > stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > is not installed on this computer. > Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > is not installed on this computer. > stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > There are some external packages and perl modules, listed above, which > stag uses. This only effects the functionality which is listed above: > the rest of stag will work fine, which includes nearly all of the > core functionality. > > Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > CMUNGALL/Data-Stag-0.11.tar.gz > make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > 3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > 1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > 6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > 5/5 skipped: various reasons > t/set-attrs..........ok > 3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > 7/7 skipped: various reasons > t/xml2...............ok > 4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) > CMUNGALL/Data-Stag-0.11.tar.gz > make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at -e line 1 > make: *** [pure_site_install] Error 13 > CMUNGALL/Data-Stag-0.11.tar.gz > make install -- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > - ERROR: You chose to install Data::Stag but it failed to install > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > * Optional prerequisite Spreadsheet::ParseExcel is not installed > (wanted for parsing Excel files, used by Bio::SeqIO::excel) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite Graph is not installed > (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > * Optional prerequisite SVG::Graph is not installed > (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > * Optional prerequisite SOAP::Lite is not installed > (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > * Optional prerequisite Bio::ASN1::EntrezGene is not installed > (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Convert::Binary::C is not installed > (wanted for strider functionality, used by Bio::SeqIO::strider) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite XML::Twig is not installed > (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > * Optional prerequisite Set::Scalar is not installed > (wanted for proper operation, used by Bio::Tree::Compatible) > * Optional prerequisite XML::Parser::PerlSAX is not installed > (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > * Optional prerequisite XML::SAX::Writer is not installed > (wanted for writing xml, used by Bio::SeqIO::tigrxml) > * Optional prerequisite Clone is not installed > (wanted for cloning objects, used by Bio::Tools::Primer3) > * Optional prerequisite XML::DOM::XPath is not installed > (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > * Optional prerequisite PostScript::TextBlock is not installed > (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > BioDBGFF.................disabled > * MySQL, Pg nor Oracle DBI drivers are installed > BioDBSeqFeature_mysql....disabled > - DBD::mysql is not installed > Network..................enabled > BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > - will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > - will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # Failed test 'use Bio::Annotation::TagTree;' > # at t/Annotation/Annotation.t line 20. > # Tried to use 'Bio::Annotation::TagTree'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # Failed test 'default itext' > # at t/Annotation/Annotation.t line 307. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > > # Failed test 'itext' > # at t/Annotation/Annotation.t line 315. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > 1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > 8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > Failed 17/19 tests, 10.53% okay > 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 > 11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > 9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > 19/267 skipped: various reasons > 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 > 10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > 10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > 4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > 14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > 13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > 10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > 10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > 8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > 3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > 2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > all 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.............................ok 1/1093 > # Failed (TODO) test at t/SearchIO/blast.t line 527. > # '0.852' > # > > # '0.9' > > # Failed (TODO) test at t/SearchIO/blast.t line 528. > # '1.599' > # <= > # '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # got: '0.946' > # expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # got: undef > # expected: '31984247' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # got: undef > # expected: '88780' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # got: undef > # expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > 4/45 skipped: various reasons > 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...........................ok 1/116 > # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # expected: undef > > # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # got: '\-\.=~' > # expected: '-\?' > > # Failed (TODO) test at t/Seq/LocatableSeq.t 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 > all 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 > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > 7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > all 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..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # Failed test 'use Bio::SeqIO::chaos;' > # at t/SeqIO/chaos.t line 15. > # Tried to use 'Bio::SeqIO::chaos'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > all 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 > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # Failed (TODO) test 'primary_id' > # at t/SeqIO/gcg.t line 54. > # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > all 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 > all 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 > all 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..................................ok 1/59 > # Failed (TODO) test 'accuracies' > # at t/SeqIO/scf.t line 78. > # got: 'ARRAY(0x100ac5648)' > # expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # Failed test 'use Bio::SeqIO::swiss;' > # at t/SeqIO/swiss.t line 12. > # Tried to use 'Bio::SeqIO::swiss'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > 112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # at t/SeqTools/GuessSeqFormat.t line 71. > # got: '0' > # expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > 5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > all 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 > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > 12/16 skipped: various reasons > 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 > all 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......................skipped > all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > 12/45 skipped: various reasons > 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 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 > all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > 2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > 3/4 skipped: various reasons > 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 > 15/26 skipped: various reasons > Failed Test Stat Wstat Total Fail List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t 255 65280 28 42 8-28 > t/AlignIO/arp.t 255 65280 48 92 3-48 > t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 > t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 > t/LocalDB/Flat.t 255 65280 24 20 15-24 > t/LocalDB/Index.t 255 65280 64 66 32-64 > t/SeqIO/Handler.t 255 65280 550 1098 2-550 > t/SeqIO/chaos.t 1 256 8 1 1 > t/SeqIO/swiss.t 255 65280 240 479 1-240 > t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 > t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From wkretzsch at gmail.com Fri Jul 30 11:37:08 2010 From: wkretzsch at gmail.com (Warren W. Kretzschmar) Date: Fri, 30 Jul 2010 11:37:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Alternatively I think you might have run "make install" when what you actually wanted to run was "sudo make install". The sudo means you install everything with root rights (which you say you have). It'll ask you for a password and then it will have the rights to install into /usr/local/bin Cheers, Warren On Fri, Jul 30, 2010 at 9:54 AM, Robson de Souza wrote: > Did you try, as root, > > ./Build.pl --install_base /opt/local > > ? > > Also, check the INSTALL file at the root of the bioperl distribution. > Robson > > On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: >> Hi there >> I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. >> I am not able to complete the installation as every time I get: >> >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> ?I have tried using both methods to install into a local folder and get the same thing >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/home/users/carrieomalley/bin' >> mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. >> >> >> If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( >> >> >> Many thanks in advance >> Carrie >> >> >> >> >> >> Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL >> Checking whether your kit is complete... >> Looks good >> >> Checking prerequisites... >> ?- ERROR: Data::Stag is not installed >> (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) >> CPAN: Storable loaded ok (v2.18) >> Going to read /Users/carrieomalley/.cpan/Metadata >> ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT >> Running install for module 'Data::Stag' >> 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' >> Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok >> x Data-Stag-0.11/ >> x Data-Stag-0.11/c-ext/ >> x Data-Stag-0.11/c-ext/README.c-ext >> x Data-Stag-0.11/c-ext/staglib.c >> x Data-Stag-0.11/c-ext/staglib.h >> x Data-Stag-0.11/Changes >> x Data-Stag-0.11/Data/ >> x Data-Stag-0.11/Data/Stag/ >> x Data-Stag-0.11/Data/Stag/Arr2HTML.pm >> x Data-Stag-0.11/Data/Stag/Base.pm >> x Data-Stag-0.11/Data/Stag/BaseGenerator.pm >> x Data-Stag-0.11/Data/Stag/BaseHandler.pm >> x Data-Stag-0.11/Data/Stag/ChainHandler.pm >> x Data-Stag-0.11/Data/Stag/DTDWriter.pm >> x Data-Stag-0.11/Data/Stag/GraphHandler.pm >> x Data-Stag-0.11/Data/Stag/HashDB.pm >> x Data-Stag-0.11/Data/Stag/IndentParser.pm >> x Data-Stag-0.11/Data/Stag/IndentWriter.pm >> x Data-Stag-0.11/Data/Stag/ITextParser.pm >> x Data-Stag-0.11/Data/Stag/ITextWriter.pm >> x Data-Stag-0.11/Data/Stag/null.pm >> x Data-Stag-0.11/Data/Stag/PerlWriter.pm >> x Data-Stag-0.11/Data/Stag/PodParser.pm >> x Data-Stag-0.11/Data/Stag/SAX2Stag.pm >> x Data-Stag-0.11/Data/Stag/Simple.pm >> x Data-Stag-0.11/Data/Stag/StagDB.pm >> x Data-Stag-0.11/Data/Stag/StagI.pm >> x Data-Stag-0.11/Data/Stag/StagImpl.pm >> x Data-Stag-0.11/Data/Stag/SxprParser.pm >> x Data-Stag-0.11/Data/Stag/SxprWriter.pm >> x Data-Stag-0.11/Data/Stag/Util.pm >> x Data-Stag-0.11/Data/Stag/Writer.pm >> x Data-Stag-0.11/Data/Stag/XMLParser.pm >> x Data-Stag-0.11/Data/Stag/XMLWriter.pm >> x Data-Stag-0.11/Data/Stag/XSLHandler.pm >> x Data-Stag-0.11/Data/Stag/XSLTHandler.pm >> x Data-Stag-0.11/Data/Stag.pm >> x Data-Stag-0.11/dev/ >> x Data-Stag-0.11/dev/create-manifest.sh >> x Data-Stag-0.11/dev/data-stag.spec >> x Data-Stag-0.11/dev/mkspec.pl >> x Data-Stag-0.11/elisp/ >> x Data-Stag-0.11/elisp/itext-mode.el >> x Data-Stag-0.11/homepage/ >> x Data-Stag-0.11/homepage/archBIG.png >> x Data-Stag-0.11/homepage/dbstag-tutorial.sgml >> x Data-Stag-0.11/homepage/images/ >> x Data-Stag-0.11/homepage/images/k-schema-diagram.png >> x Data-Stag-0.11/homepage/images/rr-schema-diagram.png >> x Data-Stag-0.11/homepage/index.html >> x Data-Stag-0.11/homepage/makefile >> x Data-Stag-0.11/homepage/mk.sh >> x Data-Stag-0.11/homepage/mkpodhtml.pl >> x Data-Stag-0.11/homepage/mkscriptdoc.pl >> x Data-Stag-0.11/homepage/script-docs/ >> x Data-Stag-0.11/homepage/script-docs/selectall_html.html >> x Data-Stag-0.11/homepage/script-docs/selectall_xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html >> x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html >> x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html >> x Data-Stag-0.11/homepage/script-docs/stag-db.html >> x Data-Stag-0.11/homepage/script-docs/stag-diff.html >> x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-elcount.html >> x Data-Stag-0.11/homepage/script-docs/stag-eval.html >> x Data-Stag-0.11/homepage/script-docs/stag-filter.html >> x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-flatten.html >> x Data-Stag-0.11/homepage/script-docs/stag-grep.html >> x Data-Stag-0.11/homepage/script-docs/stag-handle.html >> x Data-Stag-0.11/homepage/script-docs/stag-ir.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-join.html >> x Data-Stag-0.11/homepage/script-docs/stag-merge.html >> x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html >> x Data-Stag-0.11/homepage/script-docs/stag-parse.html >> x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html >> x Data-Stag-0.11/homepage/script-docs/stag-query.html >> x Data-Stag-0.11/homepage/script-docs/stag-show-template.html >> x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html >> x Data-Stag-0.11/homepage/script-docs/stag-splitter.html >> x Data-Stag-0.11/homepage/script-docs/stag-storenode.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html >> x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html >> x Data-Stag-0.11/homepage/script-docs/stag-view.html >> x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html >> x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html >> x Data-Stag-0.11/homepage/script-list.html >> x Data-Stag-0.11/homepage/stag-db-tutorial.html >> x Data-Stag-0.11/homepage/stag-poster.html >> x Data-Stag-0.11/INSTALL >> x Data-Stag-0.11/Makefile.PL >> x Data-Stag-0.11/MANIFEST >> x Data-Stag-0.11/META.yml >> x Data-Stag-0.11/README >> x Data-Stag-0.11/scripts/ >> x Data-Stag-0.11/scripts/stag-autoschema.pl >> x Data-Stag-0.11/scripts/stag-db.pl >> x Data-Stag-0.11/scripts/stag-diff.pl >> x Data-Stag-0.11/scripts/stag-drawtree.pl >> x Data-Stag-0.11/scripts/stag-elcount.pl >> x Data-Stag-0.11/scripts/stag-eval.pl >> x Data-Stag-0.11/scripts/stag-filter.pl >> x Data-Stag-0.11/scripts/stag-findsubtree.pl >> x Data-Stag-0.11/scripts/stag-flatten.pl >> x Data-Stag-0.11/scripts/stag-grep.pl >> x Data-Stag-0.11/scripts/stag-handle.pl >> x Data-Stag-0.11/scripts/stag-itext2simple.pl >> x Data-Stag-0.11/scripts/stag-itext2sxpr.pl >> x Data-Stag-0.11/scripts/stag-itext2xml.pl >> x Data-Stag-0.11/scripts/stag-join.pl >> x Data-Stag-0.11/scripts/stag-merge.pl >> x Data-Stag-0.11/scripts/stag-mogrify.pl >> x Data-Stag-0.11/scripts/stag-parse.pl >> x Data-Stag-0.11/scripts/stag-query.pl >> x Data-Stag-0.11/scripts/stag-splitter.pl >> x Data-Stag-0.11/scripts/stag-view.pl >> x Data-Stag-0.11/scripts/stag-xml2itext.pl >> x Data-Stag-0.11/scripts/stag-xmlsplit.pl >> x Data-Stag-0.11/t/ >> x Data-Stag-0.11/t/animal.x >> x Data-Stag-0.11/t/autoschema.t >> x Data-Stag-0.11/t/barfly.x >> x Data-Stag-0.11/t/bio.x >> x Data-Stag-0.11/t/chainhandler.t >> x Data-Stag-0.11/t/collapse.x >> x Data-Stag-0.11/t/data/ >> x Data-Stag-0.11/t/data/attrs.xml >> x Data-Stag-0.11/t/data/bf.txt >> x Data-Stag-0.11/t/data/eco.el >> x Data-Stag-0.11/t/data/eco.itext >> x Data-Stag-0.11/t/data/homol.itext >> x Data-Stag-0.11/t/data/persons.el >> x Data-Stag-0.11/t/db.t >> x Data-Stag-0.11/t/emptytag.t >> x Data-Stag-0.11/t/get.t >> x Data-Stag-0.11/t/graph.x >> x Data-Stag-0.11/t/handlers.t >> x Data-Stag-0.11/t/handlers2.t >> x Data-Stag-0.11/t/handlers2.x >> x Data-Stag-0.11/t/hashdb.t >> x Data-Stag-0.11/t/hashdb.x >> x Data-Stag-0.11/t/homol.t >> x Data-Stag-0.11/t/lisp.x >> x Data-Stag-0.11/t/parsestr.t >> x Data-Stag-0.11/t/path.x >> x Data-Stag-0.11/t/path2.x >> x Data-Stag-0.11/t/qmatch.t >> x Data-Stag-0.11/t/roundtrip-attrs.t >> x Data-Stag-0.11/t/set-attrs.t >> x Data-Stag-0.11/t/set.t >> x Data-Stag-0.11/t/sxpr.t >> x Data-Stag-0.11/t/unhash.t >> x Data-Stag-0.11/t/unset.t >> x Data-Stag-0.11/t/write.t >> x Data-Stag-0.11/t/xml1.t >> x Data-Stag-0.11/t/xml2.t >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> >> >> External Module XML::LibXSLT, XSLT, >> ?is not installed on this computer. >> ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations >> >> External Module XML::Parser::PerlSAX, SAX Handler, >> ?is not installed on this computer. >> ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML >> >> External Module GD, Graphical Drawing Toolkit, >> ?is not installed on this computer. >> ?stag-drawtree.pl in Data::Stag needs it for drawing trees >> >> External Module Graph::Directed, Generic Graph data stucture and algorithms, >> ?is not installed on this computer. >> ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs >> >> External Module Tk, Tk, >> ?is not installed on this computer. >> ?stag-view.pl in Data::Stag needs it for tree viewer >> >> >> Information: >> >> ? There are some external packages and perl modules, listed above, which >> ? stag uses. This only effects the functionality which is listed above: >> ? the rest of stag will work fine, which includes nearly all of the >> ? core functionality. >> >> ? Enjoy the rest of stag, which you can use after going 'make install' >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Data >> Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites >> cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm >> cp Data/Stag.pm blib/lib/Data/Stag.pm >> cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm >> cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm >> cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm >> cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm >> cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm >> cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm >> cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm >> cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm >> cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm >> cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm >> cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm >> cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm >> cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm >> cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm >> cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm >> cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm >> cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm >> cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm >> cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm >> cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm >> cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm >> cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm >> cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm >> cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm >> cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm >> cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm >> cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm >> cp scripts/stag-view.pl blib/script/stag-view.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl >> cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl >> cp scripts/stag-grep.pl blib/script/stag-grep.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl >> cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl >> cp scripts/stag-merge.pl blib/script/stag-merge.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl >> cp scripts/stag-parse.pl blib/script/stag-parse.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl >> cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl >> cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl >> cp scripts/stag-join.pl blib/script/stag-join.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl >> cp scripts/stag-db.pl blib/script/stag-db.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl >> cp scripts/stag-filter.pl blib/script/stag-filter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl >> cp scripts/stag-handle.pl blib/script/stag-handle.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl >> cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl >> cp scripts/stag-query.pl blib/script/stag-query.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl >> cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl >> cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl >> cp scripts/stag-flatten.pl blib/script/stag-flatten.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl >> cp scripts/stag-splitter.pl blib/script/stag-splitter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl >> cp scripts/stag-diff.pl blib/script/stag-diff.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl >> cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl >> Manifying blib/man1/stag-view.pl.1 >> Manifying blib/man1/stag-mogrify.pl.1 >> Manifying blib/man1/stag-grep.pl.1 >> Manifying blib/man1/stag-handle.pl.1 >> Manifying blib/man1/stag-drawtree.pl.1 >> Manifying blib/man1/stag-query.pl.1 >> Manifying blib/man1/stag-merge.pl.1 >> Manifying blib/man1/stag-parse.pl.1 >> Manifying blib/man1/stag-findsubtree.pl.1 >> Manifying blib/man1/stag-join.pl.1 >> Manifying blib/man1/stag-autoschema.pl.1 >> Manifying blib/man1/stag-db.pl.1 >> Manifying blib/man1/stag-flatten.pl.1 >> Manifying blib/man1/stag-splitter.pl.1 >> Manifying blib/man1/stag-diff.pl.1 >> Manifying blib/man1/stag-filter.pl.1 >> Manifying blib/man3/Data::Stag::StagDB.3pm >> Manifying blib/man3/Data::Stag::SxprWriter.3pm >> Manifying blib/man3/Data::Stag.3pm >> Manifying blib/man3/Data::Stag::ChainHandler.3pm >> Manifying blib/man3/Data::Stag::IndentParser.3pm >> Manifying blib/man3/Data::Stag::Simple.3pm >> Manifying blib/man3/Data::Stag::SAX2Stag.3pm >> Manifying blib/man3/Data::Stag::Arr2HTML.3pm >> Manifying blib/man3/Data::Stag::XSLHandler.3pm >> Manifying blib/man3/Data::Stag::PerlWriter.3pm >> Manifying blib/man3/Data::Stag::XSLTHandler.3pm >> Manifying blib/man3/Data::Stag::DTDWriter.3pm >> Manifying blib/man3/Data::Stag::Writer.3pm >> Manifying blib/man3/Data::Stag::XMLWriter.3pm >> Manifying blib/man3/Data::Stag::GraphHandler.3pm >> Manifying blib/man3/Data::Stag::XMLParser.3pm >> Manifying blib/man3/Data::Stag::StagImpl.3pm >> Manifying blib/man3/Data::Stag::PodParser.3pm >> Manifying blib/man3/Data::Stag::BaseGenerator.3pm >> Manifying blib/man3/Data::Stag::IndentWriter.3pm >> Manifying blib/man3/Data::Stag::HashDB.3pm >> Manifying blib/man3/Data::Stag::null.3pm >> Manifying blib/man3/Data::Stag::ITextParser.3pm >> Manifying blib/man3/Data::Stag::BaseHandler.3pm >> Manifying blib/man3/Data::Stag::ITextWriter.3pm >> Manifying blib/man3/Data::Stag::SxprParser.3pm >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/autoschema.........ok >> t/chainhandler.......ok >> t/db.................ok >> t/emptytag...........ok >> ? ? ? ?3/3 skipped: various reasons >> t/get................ok >> t/handlers...........ok >> t/handlers2..........ok >> ? ? ? ?1/9 skipped: various reasons >> t/hashdb.............ok >> t/homol..............ok >> t/parsestr...........ok >> ? ? ? ?6/6 skipped: various reasons >> t/qmatch.............ok >> t/roundtrip-attrs....ok >> ? ? ? ?5/5 skipped: various reasons >> t/set-attrs..........ok >> ? ? ? ?3/3 skipped: various reasons >> t/set................ok >> t/sxpr...............ok >> t/unhash.............ok >> t/unset..............ok >> t/write..............ok >> t/xml1...............ok >> ? ? ? ?7/7 skipped: various reasons >> t/xml2...............ok >> ? ? ? ?4/4 skipped: various reasons >> All tests successful, 29 subtests skipped. >> Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make test -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make install >> Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at -e line 1 >> make: *** [pure_site_install] Error 13 >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make install ?-- NOT OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> >> *** (back in Bioperl Build.PL) *** >> Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n >> ?- ERROR: You chose to install Data::Stag but it failed to install >> ?* Optional prerequisite Ace is not installed >> ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) >> ?* Optional prerequisite Spreadsheet::ParseExcel is not installed >> ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) >> ?* Optional prerequisite Math::Random is not installed >> ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) >> ?* Optional prerequisite Graph is not installed >> ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) >> ?* Optional prerequisite SVG::Graph is not installed >> ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) >> ?* Optional prerequisite SOAP::Lite is not installed >> ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) >> ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed >> ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) >> ?* Optional prerequisite GraphViz is not installed >> ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) >> ?* Optional prerequisite Array::Compare is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite Convert::Binary::C is not installed >> ? (wanted for strider functionality, used by Bio::SeqIO::strider) >> ?* Optional prerequisite Algorithm::Munkres is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite XML::Twig is not installed >> ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) >> ?* Optional prerequisite Set::Scalar is not installed >> ? (wanted for proper operation, used by Bio::Tree::Compatible) >> ?* Optional prerequisite XML::Parser::PerlSAX is not installed >> ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) >> ?* Optional prerequisite XML::SAX::Writer is not installed >> ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) >> ?* Optional prerequisite Clone is not installed >> ? (wanted for cloning objects, used by Bio::Tools::Primer3) >> ?* Optional prerequisite XML::DOM::XPath is not installed >> ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) >> ?* Optional prerequisite PostScript::TextBlock is not installed >> ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions >> of the modules indicated above before proceeding with this installation >> >> Checking features: >> ?BioDBGFF.................disabled >> ? ?* MySQL, Pg nor Oracle DBI drivers are installed >> ?BioDBSeqFeature_mysql....disabled >> ? ?- DBD::mysql is not installed >> ?Network..................enabled >> ?BioDBSeqFeature_BDB......enabled >> >> Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] >> ?- will install all scripts >> >> Do you want to run tests that require connection to servers across the internet >> (likely to cause some failures)? y/n [n] n >> ?- will not run internet-requiring tests >> Deleting Build >> Removed previous script 'Build' >> >> Creating new 'Build' script for 'BioPerl' version '1.006000' >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> t/Align/AlignStats...........................ok >> t/Align/AlignUtil............................ok >> t/Align/SimpleAlign..........................ok >> t/Align/TreeBuild............................ok >> t/Align/Utilities............................ok >> t/AlignIO/AlignIO............................ok 1/28 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> # Looks like you planned 28 tests but only ran 7. >> # Looks like your test died just after 7. >> t/AlignIO/AlignIO............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 8-28 >> ? ? ? ?Failed 21/28 tests, 25.00% okay >> t/AlignIO/arp................................ok 1/48 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> # Looks like you planned 48 tests but only ran 2. >> # Looks like your test died just after 2. >> t/AlignIO/arp................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-48 >> ? ? ? ?Failed 46/48 tests, 4.17% okay >> 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......................ok 1/159 >> # ? Failed test 'use Bio::Annotation::TagTree;' >> # ? at t/Annotation/Annotation.t line 20. >> # ? ? Tried to use 'Bio::Annotation::TagTree'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. >> # Compilation failed in require at (eval 37) line 2. >> # BEGIN failed--compilation aborted at (eval 37) line 2. >> t/Annotation/Annotation......................NOK 9/159 >> # ? Failed test 'default itext' >> # ? at t/Annotation/Annotation.t line 307. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> >> # ? Failed test 'itext' >> # ? at t/Annotation/Annotation.t line 315. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. >> # Looks like you planned 159 tests but only ran 119. >> # Looks like you failed 3 tests of 119 run. >> # Looks like your test died just after 119. >> t/Annotation/Annotation......................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 9, 117, 119-159 >> ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) >> t/Annotation/AnnotationAdaptor...............ok >> t/Assembly/Assembly..........................ok 1/51 >> # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. >> t/Assembly/Assembly..........................ok >> t/Assembly/ContigSpectrum....................ok >> t/Biblio/Biblio..............................ok >> ? ? ? ?1/24 skipped: various reasons >> t/Biblio/References..........................ok >> t/Biblio/biofetch............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Biblio/eutils..............................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/ClusterIO/ClusterIO........................ok >> ? ? ? ?8/12 skipped: various reasons >> t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/ClusterIO/SequenceFamily.t:16 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. >> # Looks like you planned 19 tests but only ran 2. >> # Looks like your test died just after 2. >> t/ClusterIO/SequenceFamily...................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-19 >> ? ? ? ?Failed 17/19 tests, 10.53% okay >> 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 >> ? ? ? ?11/279 skipped: various reasons >> t/LocalDB/BlastIndex.........................ok >> t/LocalDB/DBFasta............................ok >> t/LocalDB/DBQual.............................ok >> t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 >> STACK: t/LocalDB/Flat.t:89 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. >> # Looks like you planned 24 tests but only ran 14. >> # Looks like your test died just after 14. >> t/LocalDB/Flat...............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-24 >> ? ? ? ?Failed 10/24 tests, 58.33% okay >> t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 >> STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 >> STACK: t/LocalDB/Index.t:91 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. >> # Looks like you planned 64 tests but only ran 31. >> # Looks like your test died just after 31. >> t/LocalDB/Index..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 32-64 >> ? ? ? ?Failed 33/64 tests, 48.44% okay >> t/LocalDB/Registry...........................ok >> ? ? ? ?9/14 skipped: various reasons >> t/LocalDB/SeqFeature.........................ok >> t/LocalDB/transfac_pro.......................ok >> t/Map/Cyto...................................ok >> t/Map/Linkage................................ok >> t/Map/Map....................................ok >> ? ? ? ?19/267 skipped: various reasons >> 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 >> ? ? ? ?10/14 skipped: various reasons >> t/Matrix/SiteMatrix..........................ok >> t/Ontology/GOterm............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/GraphAdaptor......................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/go.............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/interpro.......................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/Ontology/IO/obo............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Ontology..........................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/OntologyEngine....................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/OntologyStore.....................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Relationship......................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/RelationshipType..................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/Term..............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Perl.......................................ok >> ? ? ? ?10/29 skipped: various reasons >> 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..................................ok >> t/PopGen/Coalescent..........................ok >> t/PopGen/HtSNP...............................ok >> t/PopGen/MK..................................ok >> ? ? ? ?4/46 skipped: various reasons >> t/PopGen/PopGen..............................ok >> t/PopGen/PopGenSims..........................ok >> t/PopGen/TagHaplotype........................ok >> t/RemoteDB/BioFetch..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/CUTG..............................ok >> ? ? ? ?14/37 skipped: various reasons >> t/RemoteDB/DB................................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EMBL..............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EUtilities........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/HIV/HIV...........................ok >> ? ? ? ?13/30 skipped: various reasons >> t/RemoteDB/HIV/HIVAnnotProcessor.............ok >> t/RemoteDB/HIV/HIVQuery......................ok >> ? ? ? ?10/41 skipped: various reasons >> t/RemoteDB/HIV/HIVQueryHelper................ok >> t/RemoteDB/RefSeq............................ok >> ? ? ? ?10/16 skipped: various reasons >> t/RemoteDB/SeqHound..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqRead_fail......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqVersion........................ok >> ? ? ? ?8/10 skipped: various reasons >> t/RemoteDB/Taxonomy..........................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/Restriction/Analysis.......................ok >> t/Restriction/Gel............................ok >> t/Restriction/IO.............................ok 1/18 >> # ? Failed (TODO) test at t/Restriction/IO.t line 31. >> t/Restriction/IO.............................ok >> ? ? ? ?3/18 skipped: various reasons >> t/Root/Exception.............................ok >> t/Root/RootI.................................ok >> t/Root/RootIO................................ok >> ? ? ? ?2/31 skipped: various reasons >> t/Root/Storable..............................ok >> t/Root/Tempfile..............................ok >> t/Root/Utilities.............................ok >> t/SearchDist.................................skipped >> ? ? ? ?all 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.............................ok 1/1093 >> # ? Failed (TODO) test at t/SearchIO/blast.t line 527. >> # ? ? '0.852' >> # ? ? ? ? > >> # ? ? '0.9' >> >> # ? Failed (TODO) test at t/SearchIO/blast.t line 528. >> # ? ? '1.599' >> # ? ? ? ? <= >> # ? ? '1' >> t/SearchIO/blast.............................ok >> t/SearchIO/blast_pull........................ok 1/289 >> # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. >> # ? ? ? ? ?got: '0.946' >> # ? ? expected: '0.943' >> t/SearchIO/blast_pull........................ok >> t/SearchIO/blasttable........................ok >> t/SearchIO/blastxml..........................ok 1/298 >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. >> # ? ? ? ? ?got: undef >> # ? ? expected: '31984247' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. >> # ? ? ? ? ?got: undef >> # ? ? expected: '88780' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. >> # ? ? ? ? ?got: undef >> # ? ? expected: '49' >> t/SearchIO/blastxml..........................ok >> t/SearchIO/cross_match.......................ok >> t/SearchIO/erpin.............................ok >> t/SearchIO/exonerate.........................ok >> ? ? ? ?4/45 skipped: various reasons >> 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...........................ok 1/116 >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. >> # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' >> # ? ? expected: undef >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. >> # ? ? ? ? ?got: '\-\.=~' >> # ? ? expected: '-\?' >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature......................ok >> ? ? ? ?7/214 skipped: various reasons >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> t/SeqIO......................................ok >> t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. >> BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqIO/Handler.t:20 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. >> # Looks like you planned 550 tests but only ran 1. >> # Looks like your test died just after 1. >> t/SeqIO/Handler..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 2-550 >> ? ? ? ?Failed 549/550 tests, 0.18% okay >> t/SeqIO/MultiFile............................ok >> t/SeqIO/Multiple_fasta.......................ok >> t/SeqIO/SeqBuilder...........................ok >> t/SeqIO/Splicedseq...........................ok >> t/SeqIO/abi..................................skipped >> ? ? ? ?all 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..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/asciitree............................ok >> t/SeqIO/bsml.................................skipped >> ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed >> t/SeqIO/bsml_sax.............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/chadoxml.............................ok >> t/SeqIO/chaos................................ >> # ? Failed test 'use Bio::SeqIO::chaos;' >> # ? at t/SeqIO/chaos.t line 15. >> # ? ? Tried to use 'Bio::SeqIO::chaos'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. >> # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> # Looks like you failed 1 test of 8. >> t/SeqIO/chaos................................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED test 1 >> ? ? ? ?Failed 1/8 tests, 87.50% okay >> t/SeqIO/chaosxml.............................skipped >> ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed >> t/SeqIO/ctf..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/embl.................................ok >> t/SeqIO/entrezgene...........................skipped >> ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed >> t/SeqIO/excel................................skipped >> ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed >> t/SeqIO/exp..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/gcg..................................ok 1/17 >> # ? Failed (TODO) test 'primary_id' >> # ? at t/SeqIO/gcg.t line 54. >> # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' >> # ? ? expected: 'roa1_drome' >> t/SeqIO/gcg..................................ok >> t/SeqIO/genbank..............................ok >> t/SeqIO/interpro.............................skipped >> ? ? ? ?all 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 >> ? ? ? ?all 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 >> ? ? ? ?all 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..................................ok 1/59 >> # ? Failed (TODO) test 'accuracies' >> # ? at t/SeqIO/scf.t line 78. >> # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' >> # ? ? expected: '482' >> t/SeqIO/scf..................................ok >> t/SeqIO/strider..............................skipped >> ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed >> t/SeqIO/swiss................................ >> # ? Failed test 'use Bio::SeqIO::swiss;' >> # ? at t/SeqIO/swiss.t line 12. >> # ? ? Tried to use 'Bio::SeqIO::swiss'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. >> # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. >> # Looks like you planned 240 tests but only ran 1. >> # Looks like you failed 1 test of 1 run. >> # Looks like your test died just after 1. >> t/SeqIO/swiss................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-240 >> ? ? ? ?Failed 240/240 tests, 0.00% okay >> t/SeqIO/tab..................................ok >> t/SeqIO/table................................ok >> ? ? ? ?112/450 skipped: various reasons >> t/SeqIO/tigr.................................ok >> t/SeqIO/tigrxml..............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/tinyseq..............................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/ztr..................................skipped >> ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqTools/GuessSeqFormat.t:62 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> t/SeqTools/GuessSeqFormat....................NOK 25/49 >> # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. >> # ' >> # ? at t/SeqTools/GuessSeqFormat.t line 71. >> # ? ? ? ? ?got: '0' >> # ? ? expected: '1' >> # Looks like you planned 49 tests but ran 1 extra. >> # Looks like you failed 1 test of 50 run. >> t/SeqTools/GuessSeqFormat....................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED tests 25, 50 >> ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) >> t/SeqTools/OddCodes..........................ok >> t/SeqTools/SeqPattern........................ok >> t/SeqTools/SeqStats..........................ok >> t/SeqTools/SeqUtils..........................ok >> t/SeqTools/SeqWords..........................ok >> t/Species....................................ok >> ? ? ? ?5/21 skipped: various reasons >> t/Structure/IO...............................ok >> t/Structure/Structure........................ok >> t/Symbol.....................................ok >> t/TaxonTree..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Domcut..............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/ELM.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/GOR4................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/HNN.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Mitoprot............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/NetPhos.............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/Tools/Analysis/Protein/Scansite.t:23 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. >> # Looks like you planned 14 tests but only ran 4. >> # Looks like your test died just after 4. >> t/Tools/Analysis/Protein/Scansite............dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 5-14 >> ? ? ? ?Failed 10/14 tests, 28.57% okay >> t/Tools/Analysis/Protein/Sopma...............ok >> ? ? ? ?12/16 skipped: various reasons >> 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 >> ? ? ? ?all 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......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Run/StandAloneBlast..................ok >> ? ? ? ?12/45 skipped: various reasons >> 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 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 >> ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed >> t/Tree/Node..................................ok >> t/Tree/PhyloNetwork/Factory..................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/GraphViz.................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/MuVector.................ok >> t/Tree/PhyloNetwork/PhyloNetwork.............skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/RandomFactory............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/TreeFactory..............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/RandomTreeFactory.....................ok >> t/Tree/Tree..................................ok >> t/Tree/TreeIO................................ok >> ? ? ? ?2/74 skipped: various reasons >> t/Tree/TreeIO/lintree........................ok >> t/Tree/TreeIO/newick.........................ok >> t/Tree/TreeIO/nexus..........................ok >> t/Tree/TreeIO/nhx............................ok >> t/Tree/TreeIO/phyloxml.......................ok >> t/Tree/TreeIO/svggraph.......................ok >> ? ? ? ?3/4 skipped: various reasons >> 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 >> ? ? ? ?15/26 skipped: various reasons >> Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed >> ------------------------------------------------------------------------------- >> t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 >> t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 >> t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 >> t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 >> t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 >> t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 >> t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 >> t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 >> t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 >> t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 >> t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 >> 57 tests and 313 subtests skipped. >> Failed 11/318 test scripts. 970/17228 subtests failed. >> Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) >> Failed 11/318 test programs. 970/17228 subtests failed. >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 >> Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 >> Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 >> Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 >> Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 >> Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 >> Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 >> Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 >> Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 >> Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 >> Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 >> Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 >> Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 >> Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 >> Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 >> Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 >> Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 >> Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 >> Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 >> Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 >> Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 >> Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 >> Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 >> Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 >> Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 >> Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 >> Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 >> Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 >> Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 >> Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 >> Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 >> Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 >> Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 >> Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 >> Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 >> Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 >> Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 >> Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 >> Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 >> Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 >> Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 >> Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 >> Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 >> Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 >> Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 >> Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 >> Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 >> Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 >> Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 >> Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 >> Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 >> Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 >> Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 >> Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 >> Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 >> Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 >> Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 sdshlxh at gmail.com Fri Jul 30 13:14:23 2010 From: sdshlxh at gmail.com (Ping Yao) Date: Fri, 30 Jul 2010 12:14:23 -0500 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: please remove me from the list. From Kevin.M.Brown at asu.edu Fri Jul 30 13:29:25 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Fri, 30 Jul 2010 10:29:25 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: <1A4207F8295607498283FE9E93B775B406D682E2@EX02.asurite.ad.asu.edu> You can remove yourself by following the link at the bottom of every email. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ping Yao Sent: Friday, July 30, 2010 10:14 AM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 please remove me from the list. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Sat Jul 31 16:56:49 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sat, 31 Jul 2010 16:56:49 -0400 Subject: [Bioperl-l] SOAP Eutilities Message-ID: Hi, Bio::DB::SoapEUtilities, referred in the HOWTO on EUtilities, seems to have disappeared from the Git repository. A simple git clone git://github.com/bioperl/bioperl-live.git does not download it. Any ideas why? Robson From twaddlac at gmail.com Thu Jul 1 10:45:01 2010 From: twaddlac at gmail.com (twaddlac) Date: Thu, 1 Jul 2010 07:45:01 -0700 (PDT) Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? Message-ID: <29046535.post@talk.nabble.com> Hi, I am having a bit of trouble reading in a qual file; I would like to input the qual file into a hash but I can't seem to find a method that returns the qual sequence. Any ideas? Thank you in advance! -- View this message in context: http://old.nabble.com/Read-in-a-Qual-File-like-a-Fasta--tp29046535p29046535.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From rmb32 at cornell.edu Thu Jul 1 20:18:58 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 01 Jul 2010 17:18:58 -0700 Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? In-Reply-To: <29046535.post@talk.nabble.com> References: <29046535.post@talk.nabble.com> Message-ID: <4C2D3072.6080803@cornell.edu> You probably want to do something like: use Bio::SeqIO; my $qual_in = Bio::SeqIO->new( -format => 'qual', -file => $ARGV[0], ); while( my $q = $qual_in->next_seq ) { print "qual for ".$q->id." is: "; print "$_ " for @{ $q->qual }; print "\n"; } twaddlac wrote: > Hi, > > I am having a bit of trouble reading in a qual file; I would like to > input the qual file into a hash but I can't seem to find a method that > returns the qual sequence. Any ideas? Thank you in advance! From cjfields at illinois.edu Fri Jul 2 09:48:19 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 08:48:19 -0500 Subject: [Bioperl-l] BioPerl Switching to GitHub Organization Message-ID: <50D544D2-5F49-482F-9E7F-EB462871B380@illinois.edu> GitHub (as expected) just released their setup for organizations, including open-source projects. The announcement is here: http://github.com/blog/674-introducing-organizations I have already moved bioperl over to an organization account and have added a few co-owners of the github repository. The move is transparent, no one should notice any difference in checking out code. I'm working on reassigning teams to projects at this time, so please post here if there are any problems. chris From iatropoul at gmail.com Fri Jul 2 00:21:09 2010 From: iatropoul at gmail.com (George Iatropoulos) Date: Thu, 1 Jul 2010 21:21:09 -0700 (PDT) Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) Message-ID: Hi guys! I'd like to thank you for this important project. I currently develop a script that uses the SeqIO module to read fasta or files with other bio-formats. However your installation instructions are too difficult to be followed, or even outdated, especially for the mac platform. After trying a week I really can't install bioperl on a Snow Leopard machine (perl 5.10.0) and I tried the CPAN and the fink method. None of them works! Especially cpan seems to mess up with itself and now doesn't install anything! As for the ubuntu platform a simple command like: "sudo apt-get install bioperl" simply does the trick! However I couldn't find this simple command in your installation guidelines, and I don't really understand why I should set up a server, before installing bioperl and then follow this complicated series of instructions, to achieve something that is so simple! I understand that you try to give complete instructions for people who may be pleased with more advanced stuff, but please don't forget biology students who don't have a deep computational background. These guys like me would appreciate some simple stuff to get their job and their projects done, without needing to waste days to figure out complicated-guru stuff. Best wishes and many thanks to all of you because bioperl is really important for us! Georgios Iatropoulos From cjfields at illinois.edu Fri Jul 2 11:46:46 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 10:46:46 -0500 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: References: Message-ID: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > Hi guys! > > I'd like to thank you for this important project. I currently develop > a script that uses the SeqIO module to read fasta or files with other > bio-formats. However your installation instructions are too difficult > to be followed, or even outdated, especially for the mac platform. > > After trying a week I really can't install bioperl on a Snow Leopard > machine (perl 5.10.0) and I tried the CPAN and the fink method. None > of them works! Especially cpan seems to mess up with itself and now > doesn't install anything! That's odd. Can you send me what you are seeing? > As for the ubuntu platform a simple command like: "sudo apt-get > install bioperl" simply does the trick! > However I couldn't find this simple command in your installation > guidelines, and I don't really understand why I should set up a > server, before installing bioperl and then follow this complicated > series of instructions, to achieve something that is so simple! That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > I understand that you try to give complete instructions for people who > may be pleased with more advanced stuff, but please don't forget > biology students who don't have a deep computational background. These > guys like me would appreciate some simple stuff to get their job and > their projects done, without needing to waste days to figure out > complicated-guru stuff. We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > Best wishes and many thanks to all of you because bioperl is really > important for us! > > Georgios Iatropoulos Sorry for the troubles, and thanks for letting us know. Any additional details about installation problems are very welcome. Also, the installation page on the bioperl website is editable (it is a wiki :). So, feel free to add more detail where needed, or use the discussion page to point out problems. chris From steffen_moeller at gmx.de Fri Jul 2 12:39:00 2010 From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=) Date: Fri, 02 Jul 2010 18:39:00 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <4C2E1624.2070402@gmx.de> Hello, On 07/02/2010 05:46 PM, Chris Fields wrote: > On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > > >> Hi guys! >> >> I'd like to thank you for this important project. I currently develop >> a script that uses the SeqIO module to read fasta or files with other >> bio-formats. However your installation instructions are too difficult >> to be followed, or even outdated, especially for the mac platform. >> >> After trying a week I really can't install bioperl on a Snow Leopard >> machine (perl 5.10.0) and I tried the CPAN and the fink method. None >> of them works! Especially cpan seems to mess up with itself and now >> doesn't install anything! >> > That's odd. Can you send me what you are seeing? > > >> As for the ubuntu platform a simple command like: "sudo apt-get >> install bioperl" simply does the trick! >> However I couldn't find this simple command in your installation >> guidelines, and I don't really understand why I should set up a >> server, before installing bioperl and then follow this complicated >> series of instructions, to achieve something that is so simple! >> > That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). > this depends on the age of your distribution rather than on what is apt-get-able from various places. Debian Squeeze has 1.6.1, and so does Ubuntu since Lucid. http://packages.qa.debian.org/b/bioperl.html https://launchpad.net/ubuntu/+source/bioperl > I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > > I am CCing the Debian-Med list just in case they have some better idea here, but what I suggest if you don't want to >> I understand that you try to give complete instructions for people who >> may be pleased with more advanced stuff, but please don't forget >> biology students who don't have a deep computational background. These >> guys like me would appreciate some simple stuff to get their job and >> their projects done, without needing to waste days to figure out >> complicated-guru stuff. >> > We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > The intention of us Debian- and Ubuntu-Helpers is very much also to help you X-core guys to concentrate on whatever you want to concentrate on and by taking as many of the "cannot build this or that" questions away from you as we possibly can. From our point of view, karmic or lenny are already rather ancient. As a BioPerl developer you probably don't want to run any of the packages in your routine anyway, so there is not much of a point to update for you. But I share your concern for production sites that want to sync with your vibrant development. If one wants to stay with binaries I see apt-pinning and backports.org. If one would just add the Debian sources of unstable to the /etc/apt/sources.list, then one could also very easily create distribution-adjusted packages oneself by apt-get source -b bioperl, which would then execute "the make" for you. The original request for a pointer to the Debian/Ubuntu packages would be nice, indeed. We'll see us at BOSC next week. If there is anything you think we should do to help your experience with the distributions then please drop us a line or grep for me in Boston. The segmentation is no problem for the packaging, but possibly more so for the regular user with a biological background. Best, Steffen From kai.blin at biotech.uni-tuebingen.de Sat Jul 3 03:05:26 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Sat, 03 Jul 2010 09:05:26 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <1278140726.2833.77.camel@gonzo.home.kblin.org> On Fri, 2010-07-02 at 10:46 -0500, Chris Fields wrote: Hi Chris, > > As for the ubuntu platform a simple command like: "sudo apt-get > > install bioperl" simply does the trick! > > However I couldn't find this simple command in your installation > > guidelines, and I don't really understand why I should set up a > > server, before installing bioperl and then follow this complicated > > series of instructions, to achieve something that is so simple! > > That's b/c the bioperl that is installed with apt is not up to date. > CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for > bioperl-run (where CPAN is at v.1.6.1). As Steffen already said, the current Ubuntu version is 1.6.1, for both bioperl and bioperl-run. I don't think providing backports for Debian/Ubuntu versions wouldn't be too hard. > I would like to get the releases to a point where they are easily > packaged for apt/yum/ppm/fink/macports/whatever, so any help along > those lines is greatly appreciated. There currently is only an "automated port" of Bioperl on the openSuse Build Service (OBS). I'll probably end up looking into packaging BioPerl for SLES11, and would do that on OBS. Supporting other suse distros is trivial, other RPM-based distros are doable once you figure out the package names. I'd say if Debian, Fedora, Suse and Ubuntu are covered, you're doing pretty fine for Linux. People using more exotic distros will be used to build their own stuff anyway. :) I've got no idea about packaging for OSX. > > I understand that you try to give complete instructions for people who > > may be pleased with more advanced stuff, but please don't forget > > biology students who don't have a deep computational background. These > > guys like me would appreciate some simple stuff to get their job and > > their projects done, without needing to waste days to figure out > > complicated-guru stuff. I think some of the instructions on installing BioPerl are pretty concise and allow you to just copy&paste the commands (see the ubuntu-server install instructions). They might be a bit outdated, I didn't check that. And of course I agree that it would be nicer if you could just point your package manager at the appropriate repository and be done. However, there's only a few people working on BioPerl, and packaging can eat a lot of time, as does keeping install instructions up-to-date. Especially on install instructions, every user can help. Once you wasted days on figuring out the complicated guru-stuff, write a wiki page to explain it in a less complicated way. :) Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From maizemu at gmail.com Sat Jul 3 11:30:14 2010 From: maizemu at gmail.com (Christopher Bottoms) Date: Sat, 3 Jul 2010 10:30:14 -0500 Subject: [Bioperl-l] Fwd: Codefest 2010: Final details In-Reply-To: References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> Message-ID: I will be there first thing Wednesday morning. I'd be glad to help work on any project. On Sat, Jul 3, 2010 at 9:15 AM, Chris Fields wrote: > I will be there on the afternoon of the 7th. There are a couple of > projects one can look into for Moose and Perl 6 (Biome and BioPerl6). I > think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not > sure where that is (might be surplanted by SQLite work?). Would be nice to > talk with Mark re: the wrapper system for BioPerl as well. > > So lots of stuff to think over and plan for. Maybe we should move this to > open-bio-l, or bioperl-l? > > chris (fields) > > On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote: > > > Chris, > > > > I do not have too much experience on cloud computing, either. There > > will be quite a few people from BioPerl . We'll meet and come up with > > a plan first thing in the morning. Unless someone has a very good one > > ready for sharing... > > > > -Heikki > > > > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho > > cell: +966 545 595 849 office: +966 2 808 2429 > > > > Computational Bioscience Research Centre (CBRC), Building #2, Office > #4216 > > 4700 King Abdullah University of Science and Technology (KAUST) > > Thuwal 23955-6900, Kingdom of Saudi Arabia > > > > > > > > > > On 3 July 2010 08:36, Christopher Bottoms wrote: > >> Hi all, > >> > >> I was originally planning on working on cloud computing at the Codefest. > >> However, the 2-day cloud computing tutorial that I was going to attend > in > >> mid June was canceled. Does anyone have any programming that they would > like > >> help with? I have experience with Perl 5, including Moose, and I am > starting > >> to dabble in Perl 6. I have also programmed in Java in the past. I hear > >> Python is easy to learn, so I'd be open to working on a Python project > as > >> well. > >> > >> Thanks, > >> Christopher Bottoms > >> > >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman > wrote: > >>> > >>> Hi all; > >>> Codefest 2010 is finally here: next Wednesday and Thursday at > >>> Harvard Medical School and Massachusetts General Hospital in > >>> beautiful Boston. All of the logistics, directions and details > >>> are on the wiki page: > >>> > >>> http://www.open-bio.org/wiki/Codefest_2010 > >>> > >>> If you want the short version: show up at Harvard Medical School on > >>> Wednesday at 10am and we'll take care of the rest. Thanks to the > >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll > >>> have coffee, lunches and internet. Thanks to Steffen and Ntino, > >>> we'll have Amazon credits to utilize. And of course, there will be > >>> BBQ and drinking on Thursday night when we are finished. > >>> > >>> I'm looking forward to a fun and productive time. The general plan > >>> will be to spend a bit of time on Wednesday morning organizing > >>> ourselves into like minded groups of folks, and then commence with > >>> coding and collaborating. > >>> > >>> If you aren't able to make it and you're listed on the wiki page under > >>> participants, please do cross your name off so we have a good idea of > >>> final numbers. Likewise, if you are coming but haven't put your name up > >>> there please add it. > >>> > >>> If you are interested in helping with making software and data > >>> available on shared cloud resources, here are the latest Amazon > >>> AMIs, snapshots, and the code base: > >>> > >>> Cloud BioLinux images: > >>> 64bit: ami-d62cc4bf > >>> 32bit: ami-5423cb3d > >>> > >>> An EBS public snapshot with indexed genomes: > >>> snap-67446d0f > >>> > >>> Infrastructure: > >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/ > >>> > >>> Send an e-mail with any questions, thoughts or concerns. My phone > >>> number is 617-447-8586 in case you end up hopelessly lost somewhere > >>> in Boston and are desperate to begin programming. > >>> > >>> Looking forward to seeing everyone next Wednesday, > >>> Brad > >> > >> > > From cjfields at illinois.edu Sat Jul 3 14:23:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:23:08 -0500 Subject: [Bioperl-l] Error when Using BLAT???? In-Reply-To: References: Message-ID: <1D738754-1FA5-40CB-B805-27A3A36FF319@illinois.edu> On Jun 29, 2010, at 8:58 AM, Minh Bui wrote: > Hi everyone, > I am writing an application that allows me to search through a database > (yeast.nt*) *with a few queries (yeastquery.fasta). Here is the code: > > *use warnings;* > *use Bio::Tools::Run::Alignment::Blat;* > *use Bio::SeqIO;* > *use Bio::DB::Fasta;* > * * > *my $seqio_object = Bio::SeqIO -> new (-file => > 'C:/Users/MINH/Desktop/yeastquery.fasta', -format => 'fasta'); * > * * > *my $database = 'C:/Users/MINH/Desktop/yeast.nt';* > *my $db = Bio::DB::Fasta->new($database); * > * * > *my $factory = Bio::Tools::Run::Alignment::Blat->new(); * > * > * > *while (my $blat_object = $seqio_object -> next_seq) {** * > * my $results = $factory -> run($blat_object,$db); * > *}* > > > BUT i got this error and don't know how to fix it. I am sorry, i am new to > Perl and Bioperl. I am using window 7, Strawberry. > > > *Replacement list is longer than search list at > C:/strawberry/perl/site/lib/Bio/Range.pm line 251.* > *Use of uninitialized value in concatenation (.) or string at > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm line 251, > line 1.* The above are warnings from perl 5.12 that can be ignored (they have been fixed in bioperl-live on github). > *'-out' is not recognized as an internal or external command,* > *operable program or batch file.* > * > * > *------------- EXCEPTION: Bio::Root::Exception -------------* > *MSG: Blat call ( -out=psl C:\Users\MINH\AppData\Local\Temp\BUiXTGzYC2 > C:\Users\MINH\AppData\Local\Temp\yQK5pzgJ_z) crashed: 256 * > * > * > *STACK: Error::throw* > *STACK: Bio::Root::Root::throw > C:/strawberry/perl/site/lib/Bio/Root/Root.pm:368* > *STACK: Bio::Tools::Run::Alignment::Blat::_run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:261* > *STACK: Bio::Tools::Run::Alignment::Blat::run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:178* > *STACK: D:/eclipswp/bioperl/readfasta.pl:15* > *-----------------------------------------------------------* > > Thank you for your help. That may be a bug; I can check on it (I'm planning on setting up a BLAT pipeline here in the next few days). chris From cjfields at illinois.edu Sat Jul 3 14:27:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:27:32 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: No comments. I'm assuming this is okay to merge into master branch, so will merge in later today. chris On Jun 30, 2010, at 12:35 PM, Chris Fields wrote: > All, > > I have a branch in github (topic/species_proxy) that converts > Bio::Species into a proxy class. This appears to fix a ton of problems > introduced during the Tree/Taxonomy refactoring a few years back. > > Advantages: > > 1) No need for Scalar::Util::weaken within Bio::Species or > Bio::Tree::Node. Cleanup methods are handled during instance > destruction. > > 2) This paves the way a bit more for eventual deprecation of > Bio::Species in 1.7. > > 3) Works with bioperl-db and BioSQL as is (passes on both my local > Ubuntu 9.10 and Mac OS X 10.6), perl 5.10 and 5.12, should work with > earlier perl versions. > > Disadvantages: > > 1) For every Bio::Species, we have a Bio::Taxon, a Bio::Tree::Tree, and > a Bio::DB::Taxonomy (one instance more than the previous Bio::Species > implementation). We can probably reduce that down considerably by > creating the needed instances lazily. > > This fixes: > > bug 3017 use threads to get genbank file error > bug 2594 Bio::Species memory leak > > and possibly others: > > bug 2773 Bio::Tree::Node gets destroyed even though it is still live > > If there are no comments, I'll merge this with the master branch in the > next few days. > > ++++++++++++++++++++++++++++++++++++++++++ > > (NOTE: skip the next two paragraphs if you don't want to read nasty > implementation details) > > Bio::Species had previously inherited from Bio::Taxon, but also required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). > > The above proxy fix converts Bio::Species into a proxy class, which only > inherits the interface (Bio::Tree::NodeI), and delegates to an internal > Bio::Taxon and a Bio::Tree::Tree. Neither contained object has a > reference back to the Bio::Species instance, thus the class can perform > proper garbage collection. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at drycafe.net Sat Jul 3 16:55:30 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 3 Jul 2010 16:55:30 -0400 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > Bio::Species had previously inherited from Bio::Taxon, but also > required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sat Jul 3 19:36:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 18:36:15 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> Message-ID: <57B6FE86-FF5E-4579-B3FB-A2D7AB366117@illinois.edu> On Jul 3, 2010, at 3:55 PM, Hilmar Lapp wrote: > On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > >> Bio::Species had previously inherited from Bio::Taxon, but also required >> it to hold a Bio::Tree::Tree which contained a circular reference back >> to the Bio::Species object, thus requiring Scalar::Util::weaken. This >> has caused several hard-to-diagnose problems with premature garbage >> collection, including some issues with threads (bug 3017). > > > Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? > > -hilmar In my experience, using weaken() is a bit of a 'code smell', and in general there are nice, sane ways to work around it. The solutions I outlined for the SeqI<->SeqFeatureI suggestion I thought made sense, if you think of Bio::SeqI as really more like a Bio::SeqRecord (has-a PrimarySeqI, does hold features, annotations, etc). There are no circular refs in this case: SeqI has-a SeqFeature(s)I, via FeatureHolderI SeqI has-a PrimarySeqI SeqFeatureI has-a PrimarySeqI Nothing refers back to SeqI It's a nice design decision and a great delegation of duties: SeqFeatures shouldn't need the Seq(Record) as a whole but the just the sequence itself, present as the PrimarySeqI, therefore they are attached to that. Any sequence-specific changes (methods, attributes) should therefore be in PrimarySeqI, and if needed could be delegated to for convenience from a relevant SeqI. In this particular instance (Bio::Species), there appeared to be a need to store a ref to the Tree (containing self) in self to implement the prior Bio::Species methods, thus requiring the use of weaken(). To me this was an indication that we really needed to rethink the design of the class. Maybe the containing instance (eg: Bio::Seq in this case) needs to hold the classification (as a Tree) and cache the relevant species NodeI (a Bio::Taxon). As we're still at the stage where we are using a Bio::Species, I pushed that functionality for the time being into the Bio::Species class: it has-a Bio::NodeI and a Bio::Tree::Tree, but neither refers back to the Bio::Species. We're planning on deprecating Bio::Species in future releases anyway, and reimplementing so that Bio::Seq is storing the Tree and the Bio::Taxon species node should be easy when the time comes. Actually, this probably suggests abstracting the simplest parts of that out into a common interface, which could be switched over to Bio::Seq when needed. May work on that a bit... chris From holland at eaglegenomics.com Mon Jul 5 06:06:56 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 5 Jul 2010 11:06:56 +0100 Subject: [Bioperl-l] Job opening at Eagle Message-ID: Hi all - thought this might be of interest to you. ==== Eagle Genomics is 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. With a number of exciting new projects on the horizon we're continuing to build up our team of talented and committed experts to help us deliver them. We are currently looking for a top-class developer to work on a wide range of complex projects. The role involves a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had at least 3 years prior experience developing code for bioinformatics projects. For this Perl/Ensembl role you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. Extensive experience programming in another language, particularly Java, is a bonus but not essential. In addition to your superb technical and customer service skills, you will also: * be able to communicate clearly and proactively, * 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, * be a self-starter and good at managing your own workload and responsibilities. You will also have had hands-on experience in at least two of the following: * SQL query design, * Open-source bioinformatics toolkits such as BioPerl, BioMart, BioSQL, etc., * Amazon EC2, * VMware, * Workflow/pipeline design (preferably using eHive or Taverna), * System and user documentation, * Developing and presenting training courses for users and developers. The successful candidate would be expected to work from our offices near Cambridge. 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. We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. The closing date is 23rd July. ==== cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From davila.marcela at gmail.com Mon Jul 5 08:57:01 2010 From: davila.marcela at gmail.com (Marcela Davila) Date: Mon, 5 Jul 2010 05:57:01 -0700 (PDT) Subject: [Bioperl-l] Infernal parser Message-ID: Hi there! I was wondering where I can set a different program directory (a local directory that has a different version of the Infernal package) rather than that specified in the ENV variable to run cmsearch while using Bio::Tools::Run::Infernal. Thanks! From cjfields at illinois.edu Mon Jul 5 11:19:13 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 10:19:13 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. chris On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > Hi there! > > I was wondering where I can set a different program directory (a local > directory that has a different version of the Infernal package) rather > than that specified in the ENV variable to run cmsearch while using > Bio::Tools::Run::Infernal. > > Thanks! > _______________________________________________ > 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 Jul 5 12:18:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 11:18:30 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: <0A2DAC96-808B-4583-B9F7-DBE44F9F9F86@illinois.edu> Marcela, After taking a look again and running a few local checks, I found that setting INFERNALDIR does work after all. I committed some code so that you can also explicitly set program_dir() as well, so the order of preference is: setting program_dir() > INFERNALDIR > PATH failing if an executable isn't found in any of those. That shouldn't be necessary, though (setting INFERNALDIR in your local env should suffice). Note that the Infernal wrapper only really supports Infernal 1.0 and up now, but the older releases still support pre-1.0 if you need them. chris On Jul 5, 2010, at 10:19 AM, Chris Fields wrote: > Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. > > chris > > On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > >> Hi there! >> >> I was wondering where I can set a different program directory (a local >> directory that has a different version of the Infernal package) rather >> than that specified in the ENV variable to run cmsearch while using >> Bio::Tools::Run::Infernal. >> >> Thanks! >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Tue Jul 6 08:37:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 6 Jul 2010 13:37:05 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl Message-ID: Hello, I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the set of scripts in BioPerl. Below is what I have so far. The script works by reading in a GFF of 'repeat_region's and a fasta file of sequences. It outputs a fasta sequence file with the repeats replaced by Xs. The script clearly needs to be more configurable, but I thought I'd send it along now to see if I'm working along the right lines, or if I should be using a different approach. Comments? Cheers, Dan. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $seq_file; my $gff_file; GetOptions ( "verbose" => \$verbose, "seq=s" => \$seq_file, "gff=s" => \$gff_file, ) or die "failed to parse command line options\n"; die "fail $gff_file : $!\n" unless -s $gff_file; ## Set up the BioPerl objects my $seq_reader = Bio::SeqIO->new( -file => $seq_file, -format => 'fasta' ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => 'fasta', -width => 80 ); my $gff_reader = Bio::FeatureIO->new( -file => $gff_file, -format => 'GFF', ); #warn $seq_reader->width, "\n"; exit; ## Run my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>1){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq 'repeat_region'){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } # Debugging #last if $c > 100; } warn "read $c repeat_region features for ", scalar keys(%repeats), " sequences\n"; ## while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; print length($sequence), "\n" if $verbose > 0; for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, 'X' x ($end - $start)); } print length($sequence), "\n" if $verbose > 0; $seq->seq($sequence); $seq_writer->write_seq($seq); # Debugging; #last; } warn "OK\n"; From armendarez77 at hotmail.com Tue Jul 6 10:23:55 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 07:23:55 -0700 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From sharmashalu.bio at gmail.com Tue Jul 6 10:48:58 2010 From: sharmashalu.bio at gmail.com (shalu sharma) Date: Tue, 6 Jul 2010 10:48:58 -0400 Subject: [Bioperl-l] Intergenomic sequences Message-ID: Hi All, This is not a bioperl question but i thought someone might know the answer. Is there any package/program to find intergenic sequences? I would really appreciate your help. Thanks Shalu From bosborne11 at verizon.net Tue Jul 6 10:36:18 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:36:18 +0200 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: > > Hello, > > I'm designing degenerate primers using > Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 > Ns, but on some sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 6 10:50:25 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:50:25 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: =head1 NAME bioflat_index.pl - index sequence files using Bio::DB::Flat =head1 DESCRIPTION Create or update a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed. =head1 USAGE bioflat_index.pl file1 file2 file3... Options: --create Create or reinitialize the index. If not specified, the index must already exist. --format The format of the sequence files. Must be one of "genbank", "swissprot", "embl" or "fasta". --location Path to the directory in which the index files are stored. --dbname The symbolic name of the database to be created. --indextype Type of index to create. Either "bdb" or "flat". "binarysearch" is the same as "flat". Options can be abbreviated. For example, use -i for --indextype. The following environment variables will be used as defaults if the corresponding options are not provided: OBDA_FORMAT format of sequence file OBDA_LOCATION path to directory in which index files are stored OBDA_DBNAME name of database OBDA_INDEX type of index to create =cut On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > Hello, > > I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the > set of scripts in BioPerl. Below is what I have so far. The script > works by reading in a GFF of 'repeat_region's and a fasta file of > sequences. It outputs a fasta sequence file with the repeats replaced > by Xs. > > The script clearly needs to be more configurable, but I thought I'd > send it along now to see if I'm working along the right lines, or if I > should be using a different approach. > > Comments? > > > Cheers, > Dan. > > > > #!/usr/bin/perl -w > > use strict; > use Getopt::Long; > > use Bio::SeqIO; > use Bio::FeatureIO; > > > > ## Set options > > my $verbose = 0; > my $seq_file; > my $gff_file; > > GetOptions > ( > "verbose" => \$verbose, > "seq=s" => \$seq_file, > "gff=s" => \$gff_file, > ) > or die "failed to parse command line options\n"; > > die "fail $gff_file : $!\n" > unless -s $gff_file; > > > > ## Set up the BioPerl objects > > my $seq_reader = > Bio::SeqIO->new( -file => $seq_file, > -format => 'fasta' > ); > > my $seq_writer = > Bio::SeqIO->new( -fh => \*STDOUT, > -format => 'fasta', > -width => 80 > ); > > my $gff_reader = > Bio::FeatureIO->new( -file => $gff_file, > -format => 'GFF', > ); > > #warn $seq_reader->width, "\n"; exit; > > > > ## Run > > my (%repeats, $c); > > while ( my $feature = $gff_reader->next_feature() ) { > if($verbose>1){ > print > join("\t", #$feature, > $feature->seq_id, > $feature->type->name, > $feature->start, > $feature->end, > ), "\n"; > } > > if($feature->type->name eq 'repeat_region'){ > $c++; > push @{$repeats{ $feature->seq_id }}, > [$feature->start, > $feature->end]; > } > > # Debugging > #last if $c > 100; > } > > warn "read $c repeat_region features for ", > scalar keys(%repeats), " sequences\n"; > > > > ## > > while(my $seq = $seq_reader->next_seq){ > my $id = $seq->id; > my $sequence = $seq->seq; > > print $id, "\n" > if $verbose > 0; > > print length($sequence), "\n" > if $verbose > 0; > > for my $region (@{$repeats{ $id }}){ > my ($start, $end) = @$region; > print "$start\t$end\n" > if $verbose > 1; > > substr($sequence, $start, $end - $start, 'X' x ($end - $start)); > } > > print length($sequence), "\n" > if $verbose > 0; > > $seq->seq($sequence); > > $seq_writer->write_seq($seq); > > # Debugging; > #last; > } > > warn "OK\n"; > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From armendarez77 at hotmail.com Tue Jul 6 11:58:11 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 08:58:11 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: Hi Brian, This sort of worked. The script still dies with the same complaint when the primer sequence is 19 bases long and starts with an 'n': Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't look very DNA to me at .... However, other 19bp long sequences with 3 internal n's are allowed. Is there another way to prevent the script from dying when it comes across these sequences or should I just not allow these sequences to be processed? Thanks, Veronica Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From roy.chaudhuri at gmail.com Tue Jul 6 12:31:04 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 06 Jul 2010 17:31:04 +0100 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: <4C335A48.8000006@gmail.com> Hi Veronica, Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. Cheers. Roy. On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > > Hi Brian, > > This sort of worked. The script still dies with the same complaint > when the primer sequence is 19 bases long and starts with an 'n': > > Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > look very DNA to me at .... > > > However, other 19bp long sequences with 3 internal n's are allowed. > Is there another way to prevent the script from dying when it comes > across these sequences or should I just not allow these sequences to > be processed? > > Thanks, > > Veronica > > Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > > > > Veronica, Yes, when you're making your sequence object do something > like: -alphabet => 'dna' For example: use Bio::Seq; > > $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > PM, wrote: > Hello, > > I'm designing degenerate primers using Bio::Tools::Primer3 and > Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to > catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > Bioperl-l mailing list Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > 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 Jul 6 13:17:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 12:17:03 -0500 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <4C335A48.8000006@gmail.com> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> <4C335A48.8000006@gmail.com> Message-ID: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! chris On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > Hi Veronica, > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > Cheers. > Roy. > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: >> >> Hi Brian, >> >> This sort of worked. The script still dies with the same complaint >> when the primer sequence is 19 bases long and starts with an 'n': >> >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't >> look very DNA to me at .... >> >> >> However, other 19bp long sequences with 3 internal n's are allowed. >> Is there another way to prevent the script from dying when it comes >> across these sequences or should I just not allow these sequences to >> be processed? >> >> Thanks, >> >> Veronica >> >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com >> >> >> >> Veronica, Yes, when you're making your sequence object do something >> like: -alphabet => 'dna' For example: use Bio::Seq; >> >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 >> PM, wrote: >> Hello, >> >> I'm designing degenerate primers using Bio::Tools::Primer3 and >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some >> sequences the script dies with the following error: >> >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't >> look very DNA to me at Perl.pm line 629. >> >> >> >> I couldn't find any information on this error. Is there a way to >> catch or override it? >> >> Thank you, >> >> Veronica >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 6 14:21:10 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 11:21:10 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> References: , ,,<1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , , , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net>, , <4C335A48.8000006@gmail.com>, <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Message-ID: Thank you. The missing 'n' was the problem. Veronica > From: cjfields at illinois.edu > Date: Tue, 6 Jul 2010 12:17:03 -0500 > To: roy.chaudhuri at gmail.com > CC: bioperl-l at lists.open-bio.org; bosborne11 at verizon.net; armendarez77 at hotmail.com > Subject: Re: [Bioperl-l] 85% ATGCN > > Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! > > chris > > On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > > > Hi Veronica, > > > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > > > Cheers. > > Roy. > > > > > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > >> > >> Hi Brian, > >> > >> This sort of worked. The script still dies with the same complaint > >> when the primer sequence is 19 bases long and starts with an 'n': > >> > >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > >> look very DNA to me at .... > >> > >> > >> However, other 19bp long sequences with 3 internal n's are allowed. > >> Is there another way to prevent the script from dying when it comes > >> across these sequences or should I just not allow these sequences to > >> be processed? > >> > >> Thanks, > >> > >> Veronica > >> > >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > >> > >> > >> > >> Veronica, Yes, when you're making your sequence object do something > >> like: -alphabet => 'dna' For example: use Bio::Seq; > >> > >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > >> PM, wrote: > >> Hello, > >> > >> I'm designing degenerate primers using Bio::Tools::Primer3 and > >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > >> sequences the script dies with the following error: > >> > >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > >> look very DNA to me at Perl.pm line 629. > >> > >> > >> > >> I couldn't find any information on this error. Is there a way to > >> catch or override it? > >> > >> Thank you, > >> > >> Veronica > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >> > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From kellert at ohsu.edu Tue Jul 6 17:54:36 2010 From: kellert at ohsu.edu (Tom Keller) Date: Tue, 6 Jul 2010 14:54:36 -0700 Subject: [Bioperl-l] SeqIO tag/location question Message-ID: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Greetings, A genbank file I am working with has features: exon 37167..37302 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=24 exon 39189..39256 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=25 exon 48058..50644 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=26 When I parse it using: my $db = Bio::DB::RefSeq->new(); my $seq = $db->get_Seq_by_acc($accession); my @features = $seq->get_SeqFeatures; for my$feat_obj ( @features ) { if ($feat_obj->primary_tag eq 'exon') { print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; for my $tag ($feat_obj->get_all_tags) { for my $value ($feat_obj->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } } I get the following: primary tag: exon start: 42167 end: 42302 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 24 primary tag: exon start: 44189 end: 44256 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 25 primary tag: exon start: 53058 end: 55644 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 26 Where does the discrepancy in location (+5000) come from? thanks for your help, Tom MMI DNA Services Core Facility 4-2442 kellert at ohsu.edu RJH (CROET/BasicScience) 6339b From cjfields at illinois.edu Tue Jul 6 19:10:18 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 18:10:18 -0500 Subject: [Bioperl-l] SeqIO tag/location question In-Reply-To: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> References: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Message-ID: <0DBD5366-A92B-4A70-B882-7E8FA88A85B0@illinois.edu> RefSeq pulls the file from EBI, not from NCBI (IIRC), so maybe there is a difference between the two versions? Hard to say w/o knowing the exact accession. chris On Jul 6, 2010, at 4:54 PM, Tom Keller wrote: > Greetings, > A genbank file I am working with has features: > exon 37167..37302 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=24 > exon 39189..39256 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=25 > exon 48058..50644 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=26 > > When I parse it using: > my $db = Bio::DB::RefSeq->new(); > my $seq = $db->get_Seq_by_acc($accession); > my @features = $seq->get_SeqFeatures; > for my$feat_obj ( @features ) { > if ($feat_obj->primary_tag eq 'exon') { > print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; > for my $tag ($feat_obj->get_all_tags) { > for my $value ($feat_obj->get_tag_values($tag)) { > print " value: ", $value, "\n"; > } > } > } > } > > I get the following: > primary tag: exon start: 42167 end: 42302 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 24 > primary tag: exon start: 44189 end: 44256 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 25 > primary tag: exon start: 53058 end: 55644 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 26 > > Where does the discrepancy in location (+5000) come from? > > thanks for your help, > Tom > MMI DNA Services Core Facility > 4-2442 > kellert at ohsu.edu > RJH (CROET/BasicScience) 6339b > > > > > > > _______________________________________________ > 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 Tue Jul 6 19:14:15 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 7 Jul 2010 00:14:15 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Cheers Brian! Do you think this script will work if I allow sequence and feature '-format's to be picked by the user among all those listed as valid file formats in BioPerl? http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS Or should I stick to Fasta/GFF (or some other implementation)? Cheers, Dan. On 6 July 2010 15:50, Brian Osborne wrote: > Dan, > > There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: > > =head1 NAME > > bioflat_index.pl - index sequence files using Bio::DB::Flat > > =head1 DESCRIPTION > > ?Create or update a biological sequence database indexed with the > ?Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files > ?containing the sequence information to be indexed. > > =head1 USAGE > > ?bioflat_index.pl file1 file2 file3... > > ?Options: > > ? ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, > ? ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. > > ? ? --format ? ? The format of the sequence files. ?Must be one > ? ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". > > ? ? --location ? ? Path to the directory in which the index files > ? ? ? ? ? ? ? ? ? ? ? ? ? are stored. > > ? ? --dbname ? ? ? The symbolic name of the database to be created. > > ? ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". > ? ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". > > Options can be abbreviated. ?For example, use -i for --indextype. > > The following environment variables will be used as defaults if the > corresponding options are not provided: > > ? ? OBDA_FORMAT ? ? ?format of sequence file > ? ? OBDA_LOCATION ? ?path to directory in which index files are stored > ? ? OBDA_DBNAME ? ? ?name of database > ? ? OBDA_INDEX ? ? ? type of index to create > > =cut > > > On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > >> Hello, >> >> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >> set of scripts in BioPerl. Below is what I have so far. The script >> works by reading in a GFF of 'repeat_region's and a fasta file of >> sequences. It outputs a fasta sequence file with the repeats replaced >> by Xs. >> >> The script clearly needs to be more configurable, but I thought I'd >> send it along now to see if I'm working along the right lines, or if I >> should be using a different approach. >> >> Comments? >> >> >> Cheers, >> Dan. >> >> >> >> #!/usr/bin/perl -w >> >> use strict; >> use Getopt::Long; >> >> use Bio::SeqIO; >> use Bio::FeatureIO; >> >> >> >> ## Set options >> >> my $verbose = 0; >> my $seq_file; >> my $gff_file; >> >> GetOptions >> ?( >> ? "verbose" => \$verbose, >> ? "seq=s" => \$seq_file, >> ? "gff=s" => \$gff_file, >> ?) >> ?or die "failed to parse command line options\n"; >> >> die "fail $gff_file : $!\n" >> ?unless -s $gff_file; >> >> >> >> ## Set up the BioPerl objects >> >> my $seq_reader = >> ?Bio::SeqIO->new( -file => $seq_file, >> ? ? ? ? ? ? ? ? ?-format => 'fasta' >> ? ? ? ? ? ? ? ?); >> >> my $seq_writer = >> ?Bio::SeqIO->new( -fh => \*STDOUT, >> ? ? ? ? ? ? ? ? ?-format => 'fasta', >> ? ? ? ? ? ? ? ? ?-width => 80 >> ? ? ? ? ? ? ? ?); >> >> my $gff_reader = >> ?Bio::FeatureIO->new( -file => $gff_file, >> ? ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >> ? ? ? ? ? ? ? ? ? ?); >> >> #warn $seq_reader->width, "\n"; exit; >> >> >> >> ## Run >> >> my (%repeats, $c); >> >> while ( my $feature = $gff_reader->next_feature() ) { >> ?if($verbose>1){ >> ? ?print >> ? ? ?join("\t", #$feature, >> ? ? ? ? ?$feature->seq_id, >> ? ? ? ? ?$feature->type->name, >> ? ? ? ? ?$feature->start, >> ? ? ? ? ?$feature->end, >> ? ? ? ? ), "\n"; >> ?} >> >> ?if($feature->type->name eq 'repeat_region'){ >> ? ?$c++; >> ? ?push @{$repeats{ $feature->seq_id }}, >> ? ? ?[$feature->start, >> ? ? ? $feature->end]; >> ?} >> >> ?# Debugging >> ?#last if $c > 100; >> } >> >> warn "read $c repeat_region features for ", >> ?scalar keys(%repeats), " sequences\n"; >> >> >> >> ## >> >> while(my $seq = $seq_reader->next_seq){ >> ?my $id = $seq->id; >> ?my $sequence = $seq->seq; >> >> ?print $id, "\n" >> ? ?if $verbose > 0; >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?for my $region (@{$repeats{ $id }}){ >> ? ?my ($start, $end) = @$region; >> ? ?print "$start\t$end\n" >> ? ? ?if $verbose > 1; >> >> ? ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >> ?} >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?$seq->seq($sequence); >> >> ?$seq_writer->write_seq($seq); >> >> ?# Debugging; >> ?#last; >> } >> >> warn "OK\n"; >> _______________________________________________ >> 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 Jul 7 05:42:59 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 07 Jul 2010 11:42:59 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, In my opinion the user should be able to use any supported format as input, yes. Brian O. On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > Cheers Brian! > > Do you think this script will work if I allow sequence and feature > '-format's to be picked by the user among all those listed as valid > file formats in BioPerl? > > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats > http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS > > > Or should I stick to Fasta/GFF (or some other implementation)? > > Cheers, > Dan. > > > On 6 July 2010 15:50, Brian Osborne wrote: >> Dan, >> >> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >> >> =head1 NAME >> >> bioflat_index.pl - index sequence files using Bio::DB::Flat >> >> =head1 DESCRIPTION >> >> Create or update a biological sequence database indexed with the >> Bio::DB::Flat indexing scheme. The arguments are a list of flat files >> containing the sequence information to be indexed. >> >> =head1 USAGE >> >> bioflat_index.pl file1 file2 file3... >> >> Options: >> >> --create Create or reinitialize the index. If not specified, >> the index must already exist. >> >> --format The format of the sequence files. Must be one >> of "genbank", "swissprot", "embl" or "fasta". >> >> --location Path to the directory in which the index files >> are stored. >> >> --dbname The symbolic name of the database to be created. >> >> --indextype Type of index to create. Either "bdb" or "flat". >> "binarysearch" is the same as "flat". >> >> Options can be abbreviated. For example, use -i for --indextype. >> >> The following environment variables will be used as defaults if the >> corresponding options are not provided: >> >> OBDA_FORMAT format of sequence file >> OBDA_LOCATION path to directory in which index files are stored >> OBDA_DBNAME name of database >> OBDA_INDEX type of index to create >> >> =cut >> >> >> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >> >>> Hello, >>> >>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>> set of scripts in BioPerl. Below is what I have so far. The script >>> works by reading in a GFF of 'repeat_region's and a fasta file of >>> sequences. It outputs a fasta sequence file with the repeats replaced >>> by Xs. >>> >>> The script clearly needs to be more configurable, but I thought I'd >>> send it along now to see if I'm working along the right lines, or if I >>> should be using a different approach. >>> >>> Comments? >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> #!/usr/bin/perl -w >>> >>> use strict; >>> use Getopt::Long; >>> >>> use Bio::SeqIO; >>> use Bio::FeatureIO; >>> >>> >>> >>> ## Set options >>> >>> my $verbose = 0; >>> my $seq_file; >>> my $gff_file; >>> >>> GetOptions >>> ( >>> "verbose" => \$verbose, >>> "seq=s" => \$seq_file, >>> "gff=s" => \$gff_file, >>> ) >>> or die "failed to parse command line options\n"; >>> >>> die "fail $gff_file : $!\n" >>> unless -s $gff_file; >>> >>> >>> >>> ## Set up the BioPerl objects >>> >>> my $seq_reader = >>> Bio::SeqIO->new( -file => $seq_file, >>> -format => 'fasta' >>> ); >>> >>> my $seq_writer = >>> Bio::SeqIO->new( -fh => \*STDOUT, >>> -format => 'fasta', >>> -width => 80 >>> ); >>> >>> my $gff_reader = >>> Bio::FeatureIO->new( -file => $gff_file, >>> -format => 'GFF', >>> ); >>> >>> #warn $seq_reader->width, "\n"; exit; >>> >>> >>> >>> ## Run >>> >>> my (%repeats, $c); >>> >>> while ( my $feature = $gff_reader->next_feature() ) { >>> if($verbose>1){ >>> print >>> join("\t", #$feature, >>> $feature->seq_id, >>> $feature->type->name, >>> $feature->start, >>> $feature->end, >>> ), "\n"; >>> } >>> >>> if($feature->type->name eq 'repeat_region'){ >>> $c++; >>> push @{$repeats{ $feature->seq_id }}, >>> [$feature->start, >>> $feature->end]; >>> } >>> >>> # Debugging >>> #last if $c > 100; >>> } >>> >>> warn "read $c repeat_region features for ", >>> scalar keys(%repeats), " sequences\n"; >>> >>> >>> >>> ## >>> >>> while(my $seq = $seq_reader->next_seq){ >>> my $id = $seq->id; >>> my $sequence = $seq->seq; >>> >>> print $id, "\n" >>> if $verbose > 0; >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> for my $region (@{$repeats{ $id }}){ >>> my ($start, $end) = @$region; >>> print "$start\t$end\n" >>> if $verbose > 1; >>> >>> substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>> } >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> $seq->seq($sequence); >>> >>> $seq_writer->write_seq($seq); >>> >>> # Debugging; >>> #last; >>> } >>> >>> warn "OK\n"; >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From gb7 at sanger.ac.uk Wed Jul 7 10:41:13 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Wed, 07 Jul 2010 15:41:13 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes Message-ID: <4C349209.6030209@sanger.ac.uk> Hi. I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? Thanks. Greg. -- 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 heikki.lehvaslaiho at gmail.com Wed Jul 7 13:14:21 2010 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 7 Jul 2010 20:14:21 +0300 Subject: [Bioperl-l] BLAT Howto? In-Reply-To: References: Message-ID: There are BLAT and SSAHA that have been around for some time. For next gen sequences, there are more algorithms coming up all the time. Have a look at e.g. Li and Homer in Briefings in Bioinformatics "A survey of sequence alignment algorithms for next-generation sequencing". -Heikki On 28 June 2010 16:15, Minh Bui wrote: > Hi everyone, > I am new to Bioperl and perl itself and running perl on window 7. > > ?My job is to develop an application that can search through a ?database > with thousands of queries. BLAT is a ?best option (if you know any other > algorithm that can do this, please let me know). I have been searching > through Bioperl BLAT documentation and there is only one document for BLAT > but without example. > I am wondering if anyone has done BLAT using Bioperl, please show me how to > use BLAT in ?Bioperl. > > Thank you very much and sorry for my english. Its not my first language. > _______________________________________________ > 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 Jul 7 22:36:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jul 2010 21:36:22 -0500 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: It is possible our NEXUS parser doesn't do this for some reason, but we would need a sample file to work out the problem. You could try Rutger Vos's Bio::Phylo, which may have this working. chris On Jul 7, 2010, at 9:41 AM, Greg Baillie wrote: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. > > In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. > > Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? > > Thanks. > > Greg. > > > > -- > 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. _______________________________________________ > 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 Jul 8 00:27:56 2010 From: jason at bioperl.org (Jason Stajich) Date: Wed, 07 Jul 2010 21:27:56 -0700 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: <4C3553CC.8030400@bioperl.org> Hi - Is this just that you have internal nodes labeled with the bootstrap/posterior value? If so you just want the node ids for the internal nodes then. The semantics of what is encoded in the internal nodes is not forced by the nexus format so it assumes they are ids by default. You can call $tree->move_id_to_bootstrap to migrate the ids of internal nodes to the bootstrap option. you can also use the -internal_node_id => 'bootstrap' option when initializing TreeIO objects too: =head2 new Title : new Usage : my $obj = Bio::TreeIO->new(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args : a hash. useful keys: -format : Specify the format of the file. Supported formats: newick Newick tree format nexus Nexus tree format nhx NHX tree format svggraph SVG graphical representation of tree tabtree ASCII text representation of tree lintree lintree output format -internal_node_id : what is stored in the internal node ids, bootstrap values or ids, coded as 'bootstrap' or 'id' -jason Greg Baillie wrote, On 7/7/10 7:41 AM: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of > trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I > iterate through the nodes looking for posterior values (/if ( > $node->has_tag('posterior') ) {.../), none of the nodes seem to have > posteriors. > > In fact, none of the nodes have any tags (/my @tags = > $node->get_all_tags(); print join ',', @tags/). And when I dump an > entire tree using Data::Dumper, there is no sign of any of the node > values. > > Does TreeIO handle these values? If so, should I be looking somewhere > other than the tags for the values? > > Thanks. > > Greg. From gb7 at sanger.ac.uk Thu Jul 8 10:24:14 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Thu, 08 Jul 2010 15:24:14 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C3553CC.8030400@bioperl.org> References: <4C349209.6030209@sanger.ac.uk> <4C3553CC.8030400@bioperl.org> Message-ID: <4C35DF8E.1050905@sanger.ac.uk> Hi Jason. I'm trying to get access to the posterior probability value, rate, etc, that are stored within open-square-bracket-ampersand and close-square-bracket ([&]) blocks in the tree string. It appears that this information is stripped out during the parsing of the tree string (I have tried to get it from the $node->bootstrap()). I'm having trouble identifying the module that parses the tree string - I thought I might be able to modify that. Any suggestions where I might find the appropriate code? In the meantime, I'll look at the Bio::Phylo modules (as per Chris' suggestion) to see if they have a way of handling that info. Thanks. Greg. Jason Stajich wrote: > Hi - > > Is this just that you have internal nodes labeled with the > bootstrap/posterior value? If so you just want the node ids for the > internal nodes then. The semantics of what is encoded in the internal > nodes is not forced by the nexus format so it assumes they are ids by > default. > You can call $tree->move_id_to_bootstrap > to migrate the ids of internal nodes to the bootstrap option. > > you can also use the -internal_node_id => 'bootstrap' option when > initializing TreeIO objects too: > > =head2 new > > Title : new > Usage : my $obj = Bio::TreeIO->new(); > Function: Builds a new Bio::TreeIO object > Returns : Bio::TreeIO > Args : a hash. useful keys: > -format : Specify the format of the file. Supported formats: > > newick Newick tree format > nexus Nexus tree format > nhx NHX tree format > svggraph SVG graphical representation of tree > tabtree ASCII text representation of tree > lintree lintree output format > -internal_node_id : what is stored in the internal node ids, > bootstrap values or ids, coded as > 'bootstrap' or 'id' > > -jason > Greg Baillie wrote, On 7/7/10 7:41 AM: >> Hi. >> >> I'm trying to extract information (eg. posterior values) from nodes >> of trees generated using BEAST/treeannotator/FigTree. >> >> The trees, which are in nexus format, seem to load OK, but when I >> iterate through the nodes looking for posterior values (/if ( >> $node->has_tag('posterior') ) {.../), none of the nodes seem to have >> posteriors. >> >> In fact, none of the nodes have any tags (/my @tags = >> $node->get_all_tags(); print join ',', @tags/). And when I dump an >> entire tree using Data::Dumper, there is no sign of any of the node >> values. >> >> Does TreeIO handle these values? If so, should I be looking somewhere >> other than the tags for the values? >> >> Thanks. >> >> Greg. -- 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 dan.bolser at gmail.com Thu Jul 8 10:33:19 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 15:33:19 +0100 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) Message-ID: The bugtracker seems broken (or taking a painfully long time to log me in). So here is my bug report before I forget: Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace Body: The code had inconsistent use of the '_qualify' function, and one instance of a hard-coded table name. These issues were not apparent until "-namespace anything" was used. First I got the fatal error: DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 428, line 2. which was due to a hard-coded table name. Then, after fixing, I got the error: Loading bulk data into database...DBD::mysql::db do failed: Table 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 570, line 10000. i.e. the prefix was being added to the table name twice. I went through the code and tried to make all references to table names consistent to ensure that bugs like this won't creep in again... however, the code for this module isn't very consistent. (See patch attached). -------------- next part -------------- A non-text attachment was scrubbed... Name: mysql.pm.patch Type: text/x-patch Size: 11908 bytes Desc: not available URL: From dan.bolser at gmail.com Thu Jul 8 12:06:59 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 17:06:59 +0100 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) Message-ID: Editing subject to see if it gets through... On 8 July 2010 15:33, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > From lincoln.stein at gmail.com Thu Jul 8 12:24:38 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:24:38 -0400 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) In-Reply-To: References: Message-ID: My code is never very consistent, unfortunately. Thanks for the patch, but it wasn't attached to the forwarded email. Could you try again? Lincoln On Thu, Jul 8, 2010 at 12:06 PM, Dan Bolser wrote: > Editing subject to see if it gets through... > > On 8 July 2010 15:33, Dan Bolser wrote: > > The bugtracker seems broken (or taking a painfully long time to log me > > in). So here is my bug report before I forget: > > > > > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > > > Body: > > The code had inconsistent use of the '_qualify' function, and one > > instance of a hard-coded table name. These issues were not apparent > > until "-namespace anything" was used. > > > > First I got the fatal error: > > > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 428, line 2. > > > > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > > > Loading bulk data into database...DBD::mysql::db do failed: Table > > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 570, line 10000. > > > > > > i.e. the prefix was being added to the table name twice. > > > > > > I went through the code and tried to make all references to table > > names consistent to ensure that bugs like this won't creep in again... > > however, the code for this module isn't very consistent. > > > > (See patch attached). > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform 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 Thu Jul 8 12:28:14 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:28:14 -0400 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) In-Reply-To: References: Message-ID: Never mind. I found the patch in the earlier message. Thanks again for tracking down the issues. Lincoln On Thu, Jul 8, 2010 at 10:33 AM, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From David.Messina at sbc.su.se Thu Jul 8 14:27:13 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jul 2010 14:27:13 -0400 Subject: [Bioperl-l] added -type for Bio::Annotation::DBLink Message-ID: Hi everybody, In working on representing sequence metadata*, I've found it useful to track the type of information that is involved in a database cross-reference. I'm adding an optional -type property to Bio::Annotation::DBLink to support this cleanly in BioPerl. Here follows my rationale. I'm not tied to doing this in B:A::DBLink if there's a better way ? it just seems the best route to me at the moment. -- So, what do I mean by tracking the type of information in a DB crossreference? Right now, a standard DBLink contains database => RefSeq ID => NM_12345 along with a few other optional properties. See the docs for details: http://doc.bioperl.org/bioperl-live/Bio/Annotation/DBLink.html I want to be able to say database => RefSeq ID => NM_12345 type => RNA Why? Two reasons: 1. a single database can store more than one type of information. RefSeq, for example, stores RNA and protein records. Although RefSeq's IDs are named intelligently to note their type (NM_xxx for transcript, NP_xxx for protein), this is not true for all databases and not everybody knows the ID codes. For example, here are three database-ID pairs: Genbank: AK291692.1 Genbank: CH471055.1 Genbank: AAH14616.1 Those are three different record types (mRNA, genomic DNA, protein) from the same database. 2. There can be multiple crossreferences for multiple types of information. There can be multiple source databases providing the same type of crossreference and multiple types of crossreferences. Take this example: Genbank: AAA81779.1 EMBL: AK291692 Ensembl: ENST00000308775 HPA: CAB001960 Two of these are mRNA records, one is a protein record, and one is something else entirely. If I wanted to take one mRNA xref and one protein xref from this set, I couldn't do it using solely the information provided above. If I had type information, though, it'd be easy. And since -type is an optional parameter, it is fully backwards-compatible. Any thoughts or comments? Dave * specifically, in SeqXML. See http://seqxml.org and http://doc.bioperl.org/bioperl-live/Bio/SeqIO/seqxml.html From abhishek.vit at gmail.com Fri Jul 9 11:02:09 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jul 2010 11:02:09 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO Message-ID: Hi (Chris) I feel I might be hitting a bug or missing something. I am trying to convert a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO for more clarity. I think the quality line is missing and the read is breaking into two lines. Any obvious mistakes ? Thanks! -Abhi ## Reading the FASTQ ASCII-64 file my $in = Bio::SeqIO->new( -format => 'fastq', -variant => 'illumina', -file => "<$in_fastq_file", ); ## File Handle for writing ASCII-33 (sanger) standard format my $out = Bio::SeqIO->new ( -format => 'fastq', -variant => 'sanger', -file => ">$out_fastq_file", ); while (my $oneread = $in->next_seq){ $out->write_seq($oneread); } Output: >HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCA AGGATATTGGTCTAA Input: @HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCAAGGATATTGGTCTAA +HWI-EAS397_0006:6:1:1023:19461#0/1 ^aYa^\a^aaaa\]a^^^^^]]]^L^Y]]]aa\`YZ^a]]a[a^^^^^`I^^^`]aaaa]]^]R`W^``^BBBBB From snoze.pa at gmail.com Fri Jul 9 15:06:31 2010 From: snoze.pa at gmail.com (snoze pa) Date: Fri, 9 Jul 2010 14:06:31 -0500 Subject: [Bioperl-l] MSG: Unrecognized DBSOURCE data: pdb: molecule Message-ID: Dear Users, While adding a genebank file to bioperl biosql database i am getting following error. Any Idea or help will be highly appreciated. Thank you s --------------------- WARNING --------------------- MSG: Unrecognized DBSOURCE data: pdb: molecule From biopython at maubp.freeserve.co.uk Sat Jul 10 07:43:47 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:43:47 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: > Hi (Chris) > > I feel I might be hitting a bug or missing something. I am trying to convert > a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO > for more clarity. I think the quality line is missing and the read is > breaking into two lines. > > Any obvious mistakes ? > > Thanks! > -Abhi It looks like you are getting FASTQ out rather than FASTQ (notice in addition to missing the qualities, the record starts with ">" rather than "@". Strange, as you do seem to be using the right FASTQ format and variant names. You could try using format="fastq-sanger" and format="fastq-illumina" rather than setting variant, to see if that changes anything. Peter From biopython at maubp.freeserve.co.uk Sat Jul 10 07:44:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:44:48 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: > On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >> Hi (Chris) >> >> I feel I might be hitting a bug or missing something. I am trying to convert >> a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO >> for more clarity. I think the quality line is missing and the read is >> breaking into two lines. >> >> Any obvious mistakes ? >> >> Thanks! >> -Abhi > > It looks like you are getting FASTQ out rather than FASTQ (notice in addition to > missing the qualities, the record starts with ">" rather than "@". Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) Peter From cjfields at illinois.edu Sat Jul 10 15:23:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jul 2010 14:23:30 -0500 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Jul 10, 2010, at 6:44 AM, Peter wrote: > On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >>> Hi (Chris) >>> >>> I feel I might be hitting a bug or missing something. I am trying to convert >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO >>> for more clarity. I think the quality line is missing and the read is >>> breaking into two lines. >>> >>> Any obvious mistakes ? >>> >>> Thanks! >>> -Abhi >> >> It looks like you are getting FASTQ out rather than FASTQ (notice in addition to >> missing the qualities, the record starts with ">" rather than "@". > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) > > Peter You have to be using a version of BioPerl that supports this. The previous version of the FASTQ parser released prior to refactoring returned FASTA when using write_seq(), which was a significant bug that was fixed during the complete overhaul prior to the FASTQ paper. My guess is the version of BioPerl is old and this is the module version being used. chris PS - Peter, had several very good mentions of this work from all Bio*/EMBOSS talks at BOSC, so a great success! From abhishek.vit at gmail.com Sat Jul 10 16:38:06 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Sat, 10 Jul 2010 16:38:06 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: Thanks guys. Time to update my Bioperl. I will do that and report if I face issues. -A On Sat, Jul 10, 2010 at 3:23 PM, Chris Fields wrote: > On Jul 10, 2010, at 6:44 AM, Peter wrote: > > > On Sat, Jul 10, 2010 at 12:43 PM, Peter > wrote: > >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap > wrote: > >>> Hi (Chris) > >>> > >>> I feel I might be hitting a bug or missing something. I am trying to > convert > >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code > and IO > >>> for more clarity. I think the quality line is missing and the read is > >>> breaking into two lines. > >>> > >>> Any obvious mistakes ? > >>> > >>> Thanks! > >>> -Abhi > >> > >> It looks like you are getting FASTQ out rather than FASTQ (notice in > addition to > >> missing the qualities, the record starts with ">" rather than "@". > > > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close > together ;) > > > > Peter > > You have to be using a version of BioPerl that supports this. The previous > version of the FASTQ parser released prior to refactoring returned FASTA > when using write_seq(), which was a significant bug that was fixed during > the complete overhaul prior to the FASTQ paper. My guess is the version of > BioPerl is old and this is the module version being used. > > chris > > PS - Peter, had several very good mentions of this work from all > Bio*/EMBOSS talks at BOSC, so a great success! From pengyu.ut at gmail.com Sat Jul 10 21:40:47 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sat, 10 Jul 2010 20:40:47 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) Message-ID: Hi, I have the following warnings and perl program. I don't understand why there is a warning and what the error is. The ncbi's eutils url seems OK. If shrink $term (see the code), then the warning is gone. Could somebody let me know what the problem is with my bioperl code? http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 $ ./main.pl |head --------------------- WARNING --------------------- MSG: NCBI esearch Errors/Warnings: Error : --------------------------------------------------- 241 2412410 20616305 20581223 20572313 20564721 20554763 20542744 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::DB::EUtilities; my $factory = Bio::DB::EUtilities->new( -eutil => 'esearch', -db => 'pubmed', -email => 'mymail at foo.bar', #-term => 'anoxia[mh] AND neoplasms[mh]', #-term => 'small ubiquitin-related modifier proteins[mh]', -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR hCaCC-1[tiab]', #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink $term, then the warning is gone. -retmode => 'xml', -retmax => 1000000, ); print $factory->get_retmax,"\n"; print $factory->get_Response->content; -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 11:14:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 10:14:54 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: Message-ID: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > Hi, > > I have the following warnings and perl program. I don't understand why > there is a warning and what the error is. The ncbi's eutils url seems > OK. If shrink $term (see the code), then the warning is gone. Could > somebody let me know what the problem is with my bioperl code? > > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 > > $ ./main.pl |head > > --------------------- WARNING --------------------- > MSG: NCBI esearch Errors/Warnings: > Error : > --------------------------------------------------- > 241 > > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> > 2412410 > 20616305 > 20581223 > 20572313 > 20564721 > 20554763 > 20542744 > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::DB::EUtilities; > > my $factory = Bio::DB::EUtilities->new( > -eutil => 'esearch', > -db => 'pubmed', > -email => 'mymail at foo.bar', > #-term => 'anoxia[mh] AND neoplasms[mh]', > #-term => 'small ubiquitin-related modifier proteins[mh]', > -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] > OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR > hCaCC-1[tiab]', > #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink > $term, then the warning is gone. > -retmode => 'xml', > -retmax => 1000000, > ); > > print $factory->get_retmax,"\n"; > print $factory->get_Response->content; > > > -- > Regards, > Peng The above XML output from that query isn't complete; you left out: CLCRG1[tiab]FLJ95147[tiab] It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. I can take a look, but the error is pretty obvious from that output (can't find those phrases). chris From pengyu.ut at gmail.com Sun Jul 11 15:54:20 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 14:54:20 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 10:14 AM, Chris Fields wrote: > On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > >> Hi, >> >> I have the following warnings and perl program. I don't understand why >> there is a warning and what the error is. The ncbi's eutils url seems >> OK. If shrink $term (see the code), then the warning is gone. Could >> somebody let me know what the problem is with my bioperl code? >> >> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 >> >> $ ./main.pl |head >> >> --------------------- WARNING --------------------- >> MSG: NCBI esearch Errors/Warnings: >> Error : >> --------------------------------------------------- >> 241 >> >> > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> >> 2412410 >> ? ? ? ? ? ? ? 20616305 >> ? ? ? ? ? ? ? 20581223 >> ? ? ? ? ? ? ? 20572313 >> ? ? ? ? ? ? ? 20564721 >> ? ? ? ? ? ? ? 20554763 >> ? ? ? ? ? ? ? 20542744 >> $ cat main.pl >> #!/usr/bin/env perl >> >> use strict; >> use warnings; >> use Bio::DB::EUtilities; >> >> my $factory = Bio::DB::EUtilities->new( >> ?-eutil => 'esearch', >> ?-db => 'pubmed', >> ?-email => 'mymail at foo.bar', >> ?#-term => 'anoxia[mh] AND neoplasms[mh]', >> ?#-term => 'small ubiquitin-related modifier proteins[mh]', >> ?-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] >> OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR >> hCaCC-1[tiab]', >> ?#-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink >> $term, then the warning is gone. >> ?-retmode => 'xml', >> ?-retmax => 1000000, >> ); >> >> print $factory->get_retmax,"\n"; >> print $factory->get_Response->content; >> >> >> -- >> Regards, >> Peng > > The above XML output from that query isn't complete; you left out: > > CLCRG1[tiab]FLJ95147[tiab] > > It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. ?I can take a look, but the error is pretty obvious from that output (can't find those phrases). Is there a way to suppress such error and warning message as they are not interesting to me? (As I can always check how many pubmed ids returned to determine if the search results anything). -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 17:16:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 16:16:15 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > ... > Is there a way to suppress such error and warning message as they are > not interesting to me? (As I can always check how many pubmed ids > returned to determine if the search results anything). > > -- > Regards, > Peng Setting -verbose to -1 should work. chris From pengyu.ut at gmail.com Sun Jul 11 20:04:30 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 19:04:30 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > >> ... >> Is there a way to suppress such error and warning message as they are >> not interesting to me? (As I can always check how many pubmed ids >> returned to determine if the search results anything). >> >> -- >> Regards, >> Peng > > Setting -verbose to -1 should work. I don't see such an option in perldoc Bio::DB::EUtilities. Would you please let me know where it is documented? In fact, I don't see the document for new() in Bio::DB::EUtilities. Would you please add this to the document? Thank you! -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 20:49:37 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 19:49:37 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <98EC5021-C5BC-4568-8080-99AC1C0C95A1@illinois.edu> On Jul 11, 2010, at 7:04 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: >> >> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: >> >>> ... >>> Is there a way to suppress such error and warning message as they are >>> not interesting to me? (As I can always check how many pubmed ids >>> returned to determine if the search results anything). >>> >>> -- >>> Regards, >>> Peng >> >> Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng verbose() is a Bio::Root::Root/RootI method (all BioPerl classes inherit it), so that's the place to look. As for new(), yes I can work on that. chris From Russell.Smithies at agresearch.co.nz Sun Jul 11 21:08:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 13:08:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Take a look at the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities Details all the methods including those that are inherited. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peng Yu > Sent: Monday, 12 July 2010 12:05 p.m. > To: Chris Fields > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields > wrote: > > > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > > > >> ... > >> Is there a way to suppress such error and warning message as they are > >> not interesting to me? (As I can always check how many pubmed ids > >> returned to determine if the search results anything). > >> > >> -- > >> Regards, > >> Peng > > > > Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng > _______________________________________________ > 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 pengyu.ut at gmail.com Sun Jul 11 21:15:46 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 20:15:46 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell wrote: > Take a look at the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > > Details all the methods including those that are inherited. This is every useful when l look for an inherent method. The box titled "methods for Bio::DB::EUtilities" is too small. May I suggest to make it a little bigger? Also, the box above it takes too much space, it is better to shrink it since there in only one class. Would you please help improve the appearance a little? -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 23:45:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 22:45:48 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > wrote: >> Take a look at the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities >> >> Details all the methods including those that are inherited. > > This is every useful when l look for an inherent method. The box > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > to make it a little bigger? Also, the box above it takes too much > space, it is better to shrink it since there in only one class. Would > you please help improve the appearance a little? > > -- > Regards, > Peng Patches welcome chris From Russell.Smithies at agresearch.co.nz Mon Jul 12 00:07:28 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:07:28 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> I think you mean "on your PC the box is too small". Because BioPerl is cross-platform it shouldn't be customized to look best on specific hardware or software , for example, Windows 7 with IE9. The Deobfuscator is included in BioPerl so you are free to edit and run on your own web-server with colors and styles to suit your exacting tastes. And as Chris said, if you'd like added documentation or a web interface changed so it looks better on your PC I suggest you start writing some patches. Don't forget, the BioPerl developers are all volunteers and don't work for you!! --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Monday, 12 July 2010 3:46 p.m. > To: Peng Yu > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > > > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > > wrote: > >> Take a look at the deobfuscator: > >> http://bioperl.org/cgi- > bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&so > rt_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > >> > >> Details all the methods including those that are inherited. > > > > This is every useful when l look for an inherent method. The box > > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > > to make it a little bigger? Also, the box above it takes too much > > space, it is better to shrink it since there in only one class. Would > > you please help improve the appearance a little? > > > > -- > > Regards, > > Peng > > Patches welcome > > chris ======================================================================= 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 Russell.Smithies at agresearch.co.nz Mon Jul 12 00:27:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:27:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347F6@exchsth.agresearch.co.nz> It's all a matter of priorities and I can't see how increasing the number of rows displayed in a web interface is more important than any other items on the list http://www.bioperl.org/wiki/Project_priority_list If you feel strongly about it and you can justify the changes then submit a bug report, and a patch. --Russell > -----Original Message----- > From: Peng Yu [mailto:pengyu.ut at gmail.com] > Sent: Monday, 12 July 2010 4:15 p.m. > To: Smithies, Russell > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 11:07 PM, Smithies, Russell > wrote: > > I think you mean "on your PC the box is too small". > > Because BioPerl is cross-platform it shouldn't be customized to look > best on specific hardware or software , for example, Windows 7 with IE9. > > The Deobfuscator is included in BioPerl so you are free to edit and run > on your own web-server with colors and styles to suit your exacting > tastes. > > > > And as Chris said, if you'd like added documentation or a web interface > changed so it looks better on your PC I suggest you start writing some > patches. > > Don't forget, the BioPerl developers are all volunteers and don't work > for you!! > > This is just a suggestion. Do you think that this is an order? I > didn't mean so. My believe is that if I feel something can be > improved, maybe others think so as well. So I'm make the suggestions > for other users as well. > > You don't have to reply if it can not be done. > > -- > Regards, > Peng ======================================================================= 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 dan.bolser at gmail.com Mon Jul 12 05:34:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 10:34:47 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: OK, here is my final version. I have tested it with GFF / Fasta, and in theory it works with all installed BioPerl sequence / feature file formats, however, I haven't tested any of those. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $feature_file; my $sequence_file; my $feature_format = 'GFF'; my $sequence_format = 'Fasta'; my $feature_to_mask = 'repeat_region'; my $seq_mask_character = 'X'; GetOptions ( "verbose" => \$verbose, "feature_file|f=s" => \$feature_file, "sequence_file|s=s" => \$sequence_file, "feature_format|ff=s" => \$feature_format, "sequence_format|sf=s" => \$sequence_format, "feature_to_mask|m=s" => \$feature_to_mask, "seq_mask_character|c=s" => \$seq_mask_character, ) or die "failed to parse command line options\n"; ## Check options ## A value should be passed die usage() unless $sequence_file && $feature_file; ## The files should exist die "problem with feature file '$feature_file' : $!\n" unless -s $feature_file; die "problem with sequence file '$sequence_file' : $!\n" unless -s $sequence_file; ## The formats should be valid $feature_format = lc($feature_format); die "ERROR: feature format '$feature_format' is not supported!\n\n" unless eval( "require Bio::FeatureIO::$feature_format" ); $sequence_format = lc($sequence_format); die "ERROR: sequence format '$sequence_format' is not supported!\n\n" unless eval( "require Bio::SeqIO::$sequence_format" ); ## Erm... die "1: what are you trying to do?\n" unless $feature_to_mask; die "2: what are you trying to do?\n" unless length($seq_mask_character) == 1; =head1 NAME bp_repeat_mask_sequence.pl - mask sequence features =head1 DESCRIPTION Takes an input sequence file and a feature file, and returns the sequence with 'repeat_region' features masked out (replaced with X's). This is useful for downstream processing of the sequence file. The masked sequence is written to STDOUT. =head1 USAGE bp_repeat_mask_sequence.pl Options: -f --feature_file The file from which the sequence features will be read (for subsequent masking). -s --sequence_file The sequence file (to be masked). --ff --feature_format The format of the feature file (the default is GFF). --sf --sequence_format The format of the sequence file (the default is fasta). -m --feature_to_mask The type of feature to mask (the default is 'repeat_region'). -c --seq_mask_character The 'mask' character to use in the sequence. (the default is 'X'). -v --verbose Generate some debugging output =cut ## Set up the BioPerl objects my $gff_reader = Bio::FeatureIO->new( -file => $feature_file, -format => $feature_format ); my $seq_reader = Bio::SeqIO->new( -file => $sequence_file, -format => $sequence_format, ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => $sequence_format, ); ## Run warn "hashing features to mask\n"; my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>0){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq $feature_to_mask){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } } warn "read $c '$feature_to_mask' features for ", scalar keys(%repeats), " sequences\n"; warn "masking sequences\n"; while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; ## Do the masking for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, $seq_mask_character x ($end - $start) ); } $seq->seq($sequence); $seq_writer->write_seq($seq); } warn "done\n"; # A bit of a hack: sub usage{ `perldoc -T ./$0` } On 7 July 2010 10:42, Brian Osborne wrote: > Dan, > > In my opinion the user should be able to use any supported format as input, yes. > > Brian O. > > On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > >> Cheers Brian! >> >> Do you think this script will work if I allow sequence and feature >> '-format's to be picked by the user among all those listed as valid >> file formats in BioPerl? >> >> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats >> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS >> >> >> Or should I stick to Fasta/GFF (or some other implementation)? >> >> Cheers, >> Dan. >> >> >> On 6 July 2010 15:50, Brian Osborne wrote: >>> Dan, >>> >>> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >>> >>> =head1 NAME >>> >>> bioflat_index.pl - index sequence files using Bio::DB::Flat >>> >>> =head1 DESCRIPTION >>> >>> Create or update a biological sequence database indexed with the >>> Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files >>> containing the sequence information to be indexed. >>> >>> =head1 USAGE >>> >>> bioflat_index.pl file1 file2 file3... >>> >>> Options: >>> >>> ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, >>> ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. >>> >>> ? --format ? ? The format of the sequence files. ?Must be one >>> ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". >>> >>> ? --location ? ? Path to the directory in which the index files >>> ? ? ? ? ? ? ? ? ? ? ? ? are stored. >>> >>> ? --dbname ? ? ? The symbolic name of the database to be created. >>> >>> ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". >>> ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". >>> >>> Options can be abbreviated. ?For example, use -i for --indextype. >>> >>> The following environment variables will be used as defaults if the >>> corresponding options are not provided: >>> >>> ? OBDA_FORMAT ? ? ?format of sequence file >>> ? OBDA_LOCATION ? ?path to directory in which index files are stored >>> ? OBDA_DBNAME ? ? ?name of database >>> ? OBDA_INDEX ? ? ? type of index to create >>> >>> =cut >>> >>> >>> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >>> >>>> Hello, >>>> >>>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>>> set of scripts in BioPerl. Below is what I have so far. The script >>>> works by reading in a GFF of 'repeat_region's and a fasta file of >>>> sequences. It outputs a fasta sequence file with the repeats replaced >>>> by Xs. >>>> >>>> The script clearly needs to be more configurable, but I thought I'd >>>> send it along now to see if I'm working along the right lines, or if I >>>> should be using a different approach. >>>> >>>> Comments? >>>> >>>> >>>> Cheers, >>>> Dan. >>>> >>>> >>>> >>>> #!/usr/bin/perl -w >>>> >>>> use strict; >>>> use Getopt::Long; >>>> >>>> use Bio::SeqIO; >>>> use Bio::FeatureIO; >>>> >>>> >>>> >>>> ## Set options >>>> >>>> my $verbose = 0; >>>> my $seq_file; >>>> my $gff_file; >>>> >>>> GetOptions >>>> ( >>>> "verbose" => \$verbose, >>>> "seq=s" => \$seq_file, >>>> "gff=s" => \$gff_file, >>>> ) >>>> or die "failed to parse command line options\n"; >>>> >>>> die "fail $gff_file : $!\n" >>>> unless -s $gff_file; >>>> >>>> >>>> >>>> ## Set up the BioPerl objects >>>> >>>> my $seq_reader = >>>> Bio::SeqIO->new( -file => $seq_file, >>>> ? ? ? ? ? ? ? ?-format => 'fasta' >>>> ? ? ? ? ? ? ?); >>>> >>>> my $seq_writer = >>>> Bio::SeqIO->new( -fh => \*STDOUT, >>>> ? ? ? ? ? ? ? ?-format => 'fasta', >>>> ? ? ? ? ? ? ? ?-width => 80 >>>> ? ? ? ? ? ? ?); >>>> >>>> my $gff_reader = >>>> Bio::FeatureIO->new( -file => $gff_file, >>>> ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >>>> ? ? ? ? ? ? ? ? ?); >>>> >>>> #warn $seq_reader->width, "\n"; exit; >>>> >>>> >>>> >>>> ## Run >>>> >>>> my (%repeats, $c); >>>> >>>> while ( my $feature = $gff_reader->next_feature() ) { >>>> if($verbose>1){ >>>> ?print >>>> ? ?join("\t", #$feature, >>>> ? ? ? ?$feature->seq_id, >>>> ? ? ? ?$feature->type->name, >>>> ? ? ? ?$feature->start, >>>> ? ? ? ?$feature->end, >>>> ? ? ? ), "\n"; >>>> } >>>> >>>> if($feature->type->name eq 'repeat_region'){ >>>> ?$c++; >>>> ?push @{$repeats{ $feature->seq_id }}, >>>> ? ?[$feature->start, >>>> ? ? $feature->end]; >>>> } >>>> >>>> # Debugging >>>> #last if $c > 100; >>>> } >>>> >>>> warn "read $c repeat_region features for ", >>>> scalar keys(%repeats), " sequences\n"; >>>> >>>> >>>> >>>> ## >>>> >>>> while(my $seq = $seq_reader->next_seq){ >>>> my $id = $seq->id; >>>> my $sequence = $seq->seq; >>>> >>>> print $id, "\n" >>>> ?if $verbose > 0; >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> for my $region (@{$repeats{ $id }}){ >>>> ?my ($start, $end) = @$region; >>>> ?print "$start\t$end\n" >>>> ? ?if $verbose > 1; >>>> >>>> ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>>> } >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> $seq->seq($sequence); >>>> >>>> $seq_writer->write_seq($seq); >>>> >>>> # Debugging; >>>> #last; >>>> } >>>> >>>> warn "OK\n"; >>>> _______________________________________________ >>>> 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 Jul 12 08:42:58 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 13:42:58 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" Message-ID: Seems I still can't log bugs here: https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 Error: Artifact: Only Artifact Admins Can Modify Private ArtifactTypes Here I my bug report: I'm following the tutorial here: http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html I successfully set up and browsed the first database (going no further than #data_file). I decided to try switching from an in memory (file-based) database to a DBI::mysql database. After taking the appropriate steps (see below), I get the following error when viewing the database in GB: The landmark named ctgA is not recognized. See the help pages for suggestions. I'm not sure why the landmark is found using a memory (file-based) database, but not found when using the same GFF loaded into mysql. This is the latest bioperl-live (although I'm still struggling with git). Any hints on what might be going wrong? I've a feeling I should perhaps roll back a few versions, as I noticed some SQL errors coming from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". Cheers, Dan. 1) I loaded the GFF: bp_seqfeature_load.pl -v -v -f -c -z \ --dsn dbi:mysql:mydb:myhost \ --namespace volvox \ --summary \ -u me -p secret \ databases/volvox/volvox_remarks.gff3 2) I changed the volvox.conf file: #db_args = -adaptor memory # -dir '$HTDOCS/databases/volvox' db_args = -adaptor DBI::mysql -dsn mydb:myhost -namespace volvox -user me -pass secret From shalabh.sharma7 at gmail.com Mon Jul 12 10:56:56 2010 From: shalabh.sharma7 at gmail.com (shalabh sharma) Date: Mon, 12 Jul 2010 10:56:56 -0400 Subject: [Bioperl-l] Intergenic regions Message-ID: Hi All, I am trying to find intergenic regions/sequences in genomes. Is there any bioperl module for that ? or any other package/software available? I would really appreciate if anyone can help me out. Thanks Shalabh From awitney at sgul.ac.uk Mon Jul 12 11:37:05 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Mon, 12 Jul 2010 16:37:05 +0100 Subject: [Bioperl-l] Intergenic regions In-Reply-To: References: Message-ID: If the genomes are already annotated then I guess you could just the Bio::Seq modules to pull out the intergenic regions. If there is no annotation yet then you would need to run some kind of gene prediction software first eg Genescan, Glimmer (google will throw up several choices). cheers adam On 12 Jul 2010, at 15:56, shalabh sharma wrote: > Hi All, > I am trying to find intergenic regions/sequences in genomes. Is > there any bioperl module for that ? or any other package/software available? > > I would really appreciate if anyone can help me out. > > Thanks > Shalabh > _______________________________________________ > 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 Jul 12 12:56:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 12 Jul 2010 11:56:12 -0500 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: Message-ID: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Dan. Is this maybe something for the GBrowse list? (cc'ing there JIC) chris On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > --dsn dbi:mysql:mydb:myhost \ > --namespace volvox \ > --summary \ > -u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args = -adaptor memory > # -dir '$HTDOCS/databases/volvox' > > db_args = -adaptor DBI::mysql > -dsn mydb:myhost > -namespace volvox > -user me > -pass secret > _______________________________________________ > 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 Tue Jul 13 03:49:44 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 08:49:44 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: Cheers Chris, Is there a known good version of "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? I believe that this is one of the more common databases, so I'm surprised to find it broken. What would be the git command to roll back to a stable BioPerl / GBrowse? Sorry for the basic questions, Dan. On 12 July 2010 17:56, Chris Fields wrote: > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From mark.alston at BBSRC.AC.UK Tue Jul 13 06:47:04 2010 From: mark.alston at BBSRC.AC.UK (mark alston (TGAC)) Date: Tue, 13 Jul 2010 11:47:04 +0100 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... Message-ID: Hi, BioPerl newbie question coming up... I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. Here's my script after days of effort (I joke not): ######################################################################### use Bio::DB::Taxonomy ; my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects foreach my $nodelet (@taxa) { print $nodelet->to_string() . "\t" ; } ######################################################################### This outputs: 131567 2 1224 1236 91347 543 413496 28141 290339 If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because 2 corresponds to: bacteria (superkingdom) 1224 corresponds to: proteobacteria (phylum) etc etc 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) But how can I get the things I've underlined out via BioPerl? Many thanks, Mark ################################################ Dr Mark Alston, Computer Biologist, The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK. tel +44 (0)1603 450910 e-mail mark.alston at bbsrc.ac.uk web http://www.tgac.bbsrc.ac.uk ################################################ From cjfields at illinois.edu Tue Jul 13 08:58:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jul 2010 07:58:41 -0500 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... In-Reply-To: References: Message-ID: Change to the following: { print $nodelet->scientific_name() . "\t" ; } chris On Jul 13, 2010, at 5:47 AM, mark alston (TGAC) wrote: > Hi, > BioPerl newbie question coming up... > I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. > Here's my script after days of effort (I joke not): > ######################################################################### > use Bio::DB::Taxonomy ; > my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); > > my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; > my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; > > my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects > > foreach my $nodelet (@taxa) > { print $nodelet->to_string() . "\t" ; } > ######################################################################### > > This outputs: > 131567 2 1224 1236 91347 543 413496 28141 290339 > > If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because > 2 corresponds to: bacteria (superkingdom) > 1224 corresponds to: proteobacteria (phylum) > etc etc > 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) > > > But how can I get the things I've underlined out via BioPerl? > Many thanks, > Mark > > ################################################ > Dr Mark Alston, > Computer Biologist, > The Genome Analysis Centre, > Norwich Research Park, > Colney Lane, Norwich, NR4 7UH, UK. > > tel +44 (0)1603 450910 > e-mail mark.alston at bbsrc.ac.uk > web http://www.tgac.bbsrc.ac.uk > ################################################ > > > _______________________________________________ > 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 Tue Jul 13 13:15:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 18:15:02 +0100 Subject: [Bioperl-l] Coordinate converter? Message-ID: Hi, When one sequence exists in the context of another larger sequence (with a precise start, end and strand), what is the easiest way to convert coordinates between the two sequences? I'm guessing there is an object I can load with the appropriate information with a conversion method? However, I'm stuck for details. I have implemented sub-sequences as features, but I'm not sure what to do next. Thanks for any hints, Dan. irc://irc.freenode.net/#bioperl From armendarez77 at hotmail.com Tue Jul 13 14:00:27 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:00:27 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Message-ID: Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From randalls at bioinfo.wsu.edu Tue Jul 13 14:43:35 2010 From: randalls at bioinfo.wsu.edu (randalls at bioinfo.wsu.edu) Date: Tue, 13 Jul 2010 11:43:35 -0700 (PDT) Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: Message-ID: <108709378.25.1279046615031.JavaMail.root@mail> One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Tue Jul 13 14:38:24 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 13 Jul 2010 11:38:24 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <1A4207F8295607498283FE9E93B775B406D676E9@EX02.asurite.ad.asu.edu> And a 64-bit OS and program to be able to utilize greater than 3GB of RAM. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of randalls at bioinfo.wsu.edu Sent: Tuesday, July 13, 2010 11:44 AM To: armendarez77 at hotmail.com Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PI D28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 13 14:57:54 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:57:54 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: That would be nice, but not possible right now :) > Date: Tue, 13 Jul 2010 11:43:35 -0700 > From: randalls at bioinfo.wsu.edu > To: armendarez77 at hotmail.com > CC: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation > > One suggestion is to use a computer with a lot more memory...... > > Randall Svancara > Systems Administrator/DBA/Developer > Main Bioinformatics Laboratory > > > > ----- Original Message ----- > From: armendarez77 at hotmail.com > To: bioperl-l at lists.open-bio.org > Sent: Tuesday, July 13, 2010 11:00:27 AM > Subject: [Bioperl-l] Muscle Alignment and Memory Allocation > > Hello, > > I need to align 20-30 large full genome sequences (150,000+ bp each), > but I run out of memory. I've tried using -maxmb at the command line and > as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either > using it wrong or it's not working. > > I've also tried aligning 2 sequences at a time and then aligning those > alignments using the -profile command, but it's still too much. > > Do you have any advice on how to do such alignments? My attempts are > below. > > Thank you, > > Veronica > > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB > > Alignment not completed, cannot save. > > > > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout > 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.74 MB > > Alignment not completed, cannot save. > > > Using Bio::Tools::Run::Alignment::Muscle and -maxmb > > SCRIPT: my $inputFile = $ARGV[0]; > my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); > > my $alnObj = $factory->align($inputFile); > my $output = "output.clw"; > my $clwOut = Bio::AlignIO->new(-format=>'clustalw', > -file=>">$output.clw"); $clwOut->write_aln($alnObj); > > OUTPUT: > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.9 MB > > Alignment not completed, cannot save. > > --------------------- WARNING --------------------- > MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in > 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] > > --------------------------------------------------- > > > > > > > _________________________________________________________________ The > New Busy is not the too busy. Combine all your e-mail accounts with > Hotmail. > http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 > _______________________________________________ Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From David.Messina at sbc.su.se Tue Jul 13 15:05:16 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jul 2010 15:05:16 -0400 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4B92E3EE-1001-44EE-8D78-B3B05E78A13E@sbc.su.se> I would contact the MUSCLE authors to see what they say, but like Randall said I would suspect that you won't be able to do such a large multiple alignment in 4GB of RAM. Dave From kai.blin at biotech.uni-tuebingen.de Tue Jul 13 14:42:58 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Tue, 13 Jul 2010 20:42:58 +0200 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: Message-ID: <1279046578.2560.14.camel@gonzo.home.kblin.org> On Tue, 2010-07-13 at 11:00 -0700, armendarez77 at hotmail.com wrote: Hi Veronica, > I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. The fact that this also fails on the command line tells me that you're not running into a BioPerl problem. See my comments inline below: [...] > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB ^^^^^^^^^^ [...] > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 ^^^^^^^^^^^^ You're running out of memory at 3211.48 MB, but you're telling muscle it's fine to use 4000 MB. Maybe you might want to provide less memory to -maxmb ..... Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From jason at bioperl.org Tue Jul 13 18:41:24 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:41:24 -0700 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: Message-ID: <4C3CEB94.300@bioperl.org> Bio::Coordinate::Pair? Dan Bolser wrote, On 7/13/10 10:15 AM: > Hi, > > When one sequence exists in the context of another larger sequence > (with a precise start, end and strand), what is the easiest way to > convert coordinates between the two sequences? > > I'm guessing there is an object I can load with the appropriate > information with a conversion method? However, I'm stuck for details. > > I have implemented sub-sequences as features, but I'm not sure what to do next. > > Thanks for any hints, > Dan. > > > irc://irc.freenode.net/#bioperl > _______________________________________________ > 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 Tue Jul 13 18:44:32 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:44:32 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4C3CEC50.6010102@bioperl.org> Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: > That would be nice, but not possible right now :) > > > > >> Date: Tue, 13 Jul 2010 11:43:35 -0700 >> From: randalls at bioinfo.wsu.edu >> To: armendarez77 at hotmail.com >> CC: bioperl-l at lists.open-bio.org >> Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> One suggestion is to use a computer with a lot more memory...... >> >> Randall Svancara >> Systems Administrator/DBA/Developer >> Main Bioinformatics Laboratory >> >> >> >> ----- Original Message ----- >> From: armendarez77 at hotmail.com >> To: bioperl-l at lists.open-bio.org >> Sent: Tuesday, July 13, 2010 11:00:27 AM >> Subject: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> Hello, >> >> I need to align 20-30 large full genome sequences (150,000+ bp each), >> but I run out of memory. I've tried using -maxmb at the command line and >> as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either >> using it wrong or it's not working. >> >> I've also tried aligning 2 sequences at a time and then aligning those >> alignments using the -profile command, but it's still too much. >> >> Do you have any advice on how to do such alignments? My attempts are >> below. >> >> Thank you, >> >> Veronica >> >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3211.48 MB >> >> Alignment not completed, cannot save. >> >> >> >> Using -maxmb at the command line: >> >> $ muscle -in 07-13-2010_fullGenomes.fasta -clwout >> 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.74 MB >> >> Alignment not completed, cannot save. >> >> >> Using Bio::Tools::Run::Alignment::Muscle and -maxmb >> >> SCRIPT: my $inputFile = $ARGV[0]; >> my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); >> >> my $alnObj = $factory->align($inputFile); >> my $output = "output.clw"; >> my $clwOut = Bio::AlignIO->new(-format=>'clustalw', >> -file=>">$output.clw"); $clwOut->write_aln($alnObj); >> >> OUTPUT: >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.9 MB >> >> Alignment not completed, cannot save. >> >> --------------------- WARNING --------------------- >> MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in >> 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] >> >> --------------------------------------------------- >> >> >> >> >> >> >> _________________________________________________________________ The >> New Busy is not the too busy. Combine all your e-mail accounts with >> Hotmail. >> http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 >> _______________________________________________ Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 13 18:48:20 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:48:20 -0700 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: <4C3CED34.9050607@bioperl.org> Dan - I'm not convinced that contig:example is proper type/source for the landmarks & scaffold - i use 'scaffold:chromosome' in my data: What happens if you change the GFF3 file line from ctgA example contig 1 50000 . . . Name=ctgA to ctgA chromosome scaffold 1 50000 . . . Name=ctgA I think this can be tweaked in the config but there may be different defaults for the in memory and DBI::mysql implementation. -jason Dan Bolser wrote, On 7/13/10 12:49 AM: > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >>> Seems I still can't log bugs here: >>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >>> >>> Error: >>> Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >>> >>> >>> Here I my bug report: >>> >>> I'm following the tutorial here: >>> >>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >>> >>> >>> I successfully set up and browsed the first database (going no further >>> than #data_file). I decided to try switching from an in memory >>> (file-based) database to a DBI::mysql database. After taking the >>> appropriate steps (see below), I get the following error when viewing >>> the database in GB: >>> >>> The landmark named ctgA is not recognized. See the help pages >>> for suggestions. >>> >>> >>> I'm not sure why the landmark is found using a memory (file-based) >>> database, but not found when using the same GFF loaded into mysql. >>> >>> This is the latest bioperl-live (although I'm still struggling with git). >>> >>> Any hints on what might be going wrong? I've a feeling I should >>> perhaps roll back a few versions, as I noticed some SQL errors coming >>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> 1) I loaded the GFF: >>> >>> bp_seqfeature_load.pl -v -v -f -c -z \ >>> --dsn dbi:mysql:mydb:myhost \ >>> --namespace volvox \ >>> --summary \ >>> -u me -p secret \ >>> databases/volvox/volvox_remarks.gff3 >>> >>> >>> 2) I changed the volvox.conf file: >>> >>> #db_args = -adaptor memory >>> # -dir '$HTDOCS/databases/volvox' >>> >>> db_args = -adaptor DBI::mysql >>> -dsn mydb:myhost >>> -namespace volvox >>> -user me >>> -pass secret >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 03:38:04 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 09:38:04 +0200 Subject: [Bioperl-l] getting only the aminoacids for a domain Message-ID: Hi, with these lines I download protein sequences matching "jjjj" uniprot code. !/usr/bin/perl use lib '/sw/share/bioperl-pm588'; use Bio::SeqIO; use Bio::DB::SwissProt; $db_obj = Bio::DB::SwissProt->new; $seq_obj = $db_obj->get_Seq_by_id('jjjj'); ...from here, I cut the sequences and get only a piece of each one (with subseq, between j1 and j2 residues) $shortened = $seq_obj->subseq(j1,j2); $seq_obj->seq($shortened); $seqio_obj = Bio::SeqIO->new(-file => '>jjjj.jletra.j1_j2.fasta', -format => 'fasta' ); $seqio_obj->write_seq($seq_obj); How can I download the sequence of ONLY THOSE AMINOACIDS that match, in uniprot, in the Sequence annotation section, Feature key: Domain & Description: lectin, ANK, Sushi,... the name of a given domain ? Is there any way of downloading all the existing fasta sequences for a given domain? Thanks in advance, JR From dan.bolser at gmail.com Wed Jul 14 06:27:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 11:27:02 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <4C3CED34.9050607@bioperl.org> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: Hi Jason, Thanks for the suggestion (see below). On 13 July 2010 23:48, Jason Stajich wrote: > Dan - > I'm not convinced that contig:example is proper type/source for the > landmarks & scaffold - i use 'scaffold:chromosome' in my data: > > What happens if you change the GFF3 file line from > ctgA example contig 1 50000 . . . Name=ctgA > to > ctgA chromosome scaffold 1 50000 . . . Name=ctgA > > > I think this can be tweaked in the config but there may be different > defaults for the in memory and DBI::mysql implementation. I found that this doesn't make any difference, however, I have found more information about what causes the bug. >From my previous email you see that I use bp_seqfeature_load.pl with the "--namespace volvox" option (I should have guessed it was something to do with this). Looking closely at the resulting tables I see that the following tables are empty volvox_attribute volvox_parent2child volvox_feature volvox_interval_stats volvox_name volvox_parent2child they are not empty when created without the "--namespace x" prefix, which is why DBI::mysql 'normally' works. All the other tables: volvox_attributelist volvox_locationlist volvox_meta volvox_sequence volvox_typelist appear to be created correctly, with or without the "--namespace x" prefix. Cheers, Dan. > -jason > Dan Bolser wrote, On 7/13/10 12:49 AM: > > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > > > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > > > > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > ? ? ? ?The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > ?--dsn dbi:mysql:mydb:myhost \ > ?--namespace volvox \ > --summary \ > ?-u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args ? ? ? = -adaptor memory > # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' > > db_args ? ? ? = -adaptor DBI::mysql > ? ? ? ? ? ? ? ?-dsn mydb:myhost > ? ? ? ? ? ? ? ?-namespace volvox > ? ? ? ? ? ? ? ?-user me > ? ? ? ? ? ? ? ?-pass secret > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 06:35:17 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 12:35:17 +0200 Subject: [Bioperl-l] install cpan on mac os x Message-ID: Hi, I have found several problems when installing CPAN in Mac OS X (version 10.6.4) previous to install Bioperl. What's the best choice for installing Bioperl on Mac OS X? I had it installed by using fink, but several modules are not found, I prefer a Unix installation. Is there any trick that I have to bear in mind? Thanks, JR From awitney at sgul.ac.uk Wed Jul 14 08:09:33 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 13:09:33 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: Message-ID: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> I have always found the CPAN route the best way of installing BioPerl on OSX. If you are having problems doing this then try posting any errors and someone may be able to help adam On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > Hi, > I have found several problems when installing CPAN in Mac OS X (version > 10.6.4) previous to install Bioperl. > > What's the best choice for installing Bioperl on Mac OS X? I had it > installed by using fink, but several modules are not found, I prefer a Unix > installation. Is there any trick that I have to bear in mind? > > Thanks, > > JR > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From joseramonblas at gmail.com Wed Jul 14 09:29:53 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 15:29:53 +0200 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix When I do: >perl -MCPAN -e shell cpan> install Bundle::CPAN ...answer Yes to all... and the last lines of my installation are: t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 1. t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 255 tests but ran 2. Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) Result: FAIL Failed 67/85 test programs. 34/9260 subtests failed. make: *** [test_dynamic] Error 255 PMQS/IO-Compress-2.027.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports PMQS/IO-Compress-2.027.tar.gz Running make install make test had returned bad status, won't install without force Failed during this command: ADAMK/File-HomeDir-0.91.tar.gz : make_test NO PMQS/IO-Compress-2.027.tar.gz : make_test NO ...any hint on where my failure comes from is appreciated. More info: Mac OS X 10.4 Xcode developer tools installed Thanks, JR El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on > OSX. > > If you are having problems doing this then try posting any errors and > someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a > Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Jul 14 09:36:45 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 14:36:45 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: <74C17C09-7818-45C9-BD7C-896A74D37F17@sgul.ac.uk> looks like its failing to install PMQS/IO-Compress-2.027.tar.gz. Try installing it on its own cpan> install PMQS/IO-Compress-2.027.tar.gz On 14 Jul 2010, at 14:29, Jos? Ram?n Blas Pastor wrote: > I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > > When I do: > >perl -MCPAN -e shell > cpan> install Bundle::CPAN > > ...answer Yes to all... and the last lines of my installation are: > > t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) > Non-zero exit status: 255 > Parse errors: No plan found in TAP output > t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 29 tests but ran 1. > t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 255 tests but ran 2. > Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) > Result: FAIL > Failed 67/85 test programs. 34/9260 subtests failed. > make: *** [test_dynamic] Error 255 > PMQS/IO-Compress-2.027.tar.gz > /usr/bin/make test -- NOT OK > //hint// to see the cpan-testers results for installing this module, try: > reports PMQS/IO-Compress-2.027.tar.gz > Running make install > make test had returned bad status, won't install without force > Failed during this command: > ADAMK/File-HomeDir-0.91.tar.gz : make_test NO > PMQS/IO-Compress-2.027.tar.gz : make_test NO > > ...any hint on where my failure comes from is appreciated. > > More info: > Mac OS X 10.4 > Xcode developer tools installed > > Thanks, > > JR > > El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on OSX. > > If you are having problems doing this then try posting any errors and someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Wed Jul 14 12:33:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 17:33:47 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <4C3CEB94.300@bioperl.org> References: <4C3CEB94.300@bioperl.org> Message-ID: Brilliant! Thanks Jason. I found the example in the docs a bit confusing, so here is my version (hopefully to be built into an AGP object): #!/usr/bin/perl -w use Bio::Location::Simple; use Bio::Coordinate::Pair; my $ctg = Bio::Location::Simple-> new( -seq_id => 'ctg', -start => 1, -end => 999, -strand => +1 ); my $ctg_on_chr = Bio::Location::Simple-> new( -seq_id => 'chr', -start => 2001, -end => 2999, -strand => -1 ); my $agp = Bio::Coordinate::Pair-> new( -in => $ctg, -out => $ctg_on_chr ); my $match_on_ctg = Bio::Location::Simple-> new( -seq_id => 'hit', -start => 25, -end => 125, -strand => +1 ); print_loc( $agp->map( $match_on_ctg ) ); which gives: "chr 2875 2975 -1" I know the algorithm is simple, but it's not so simple to type it out, base perfect and bug free every time you need it. Cheers, Dan. On 13 July 2010 23:41, Jason Stajich wrote: > Bio::Coordinate::Pair? > > > Dan Bolser wrote, On 7/13/10 10:15 AM: >> >> Hi, >> >> When one sequence exists in the context of another larger sequence >> (with a precise start, end and strand), what is the easiest way to >> convert coordinates between the two sequences? >> >> I'm guessing there is an object I can load with the appropriate >> information with a conversion method? However, I'm stuck for details. >> >> I have implemented sub-sequences as features, but I'm not sure what to do >> next. >> >> Thanks for any hints, >> Dan. >> >> >> irc://irc.freenode.net/#bioperl >> _______________________________________________ >> 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 Jul 14 15:12:20 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jul 2010 13:12:20 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> Message-ID: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> On Jul 14, 2010, at 10:33, Dan Bolser wrote: > I found the example in the docs a bit confusing, Hey Dan, Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Dave From dan.bolser at gmail.com Thu Jul 15 04:42:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 09:42:12 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: On 14 July 2010 20:12, Dave Messina wrote: > > > > > On Jul 14, 2010, at 10:33, Dan Bolser wrote: > >> I found the example in the docs a bit confusing, > > > Hey Dan, > > Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Sure thing Dave. The wiki is my preferred choice because it's easy for me to edit. However, having looked a git a bit, it seems like it should be easy for me to now mod the pod. I've put my code example with comments here: http://bioperl.org/wiki/Module:Bio::Coordinate::Pair One of the main reasons that I gave up editing the wiki is the very slow response time. I'm not sure what the bottleneck could be, but page loads, history checks, open for edits, and saves all take way longer than I'd like. This is especially frustrating when you want to make minor edits. (It may be worth noting that minor edits are the way wikis work [1]). This could be a good opportunity to spam the following conference: NETTAB 2010 - Workshop on biological wikis http://www.nettab.org/2010/ Thanks again for help, Dan. [1] http://www.parc.com/publication/1749/power-of-the-few-vs-wisdom-of-the-crowd.html > Dave > From David.Messina at sbc.su.se Thu Jul 15 10:59:43 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 15 Jul 2010 08:59:43 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> > I've put my code example with comments here: > > http://bioperl.org/wiki/Module:Bio::Coordinate::Pair Great, thanks. Much appreciated. > One of the main reasons that I gave up editing the wiki is the very > slow response time. Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > NETTAB 2010 - Workshop on biological wikis > http://www.nettab.org/2010/ Ah, Naples...love that city. If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. Dave From biopython at maubp.freeserve.co.uk Thu Jul 15 11:41:32 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 16:41:32 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Thu, Jul 15, 2010 at 3:59 PM, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. > BioPerl is a volunteer project and our hosting space is donated. > There were some zombie perl crontab processes were running - Mauricio has killed them and is looking at updating/fixing them. The wiki does seem faster now :) Peter From dan.bolser at gmail.com Thu Jul 15 13:46:45 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 18:46:45 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On 15 July 2010 15:59, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. How big is the wiki database? How about moving to http://bifx.org? >> NETTAB 2010 - Workshop on biological wikis >> http://www.nettab.org/2010/ > > Ah, Naples...love that city. > > If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. > > > Dave From jovel_juan at hotmail.com Thu Jul 15 13:53:04 2010 From: jovel_juan at hotmail.com (Juan Jovel) Date: Thu, 15 Jul 2010 17:53:04 +0000 Subject: [Bioperl-l] How to convert SFF into Fastq Message-ID: Hello! How can I convert a SFF file from 454 into a Fastq format? Thanks a lot! JUAN _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline From biopython at maubp.freeserve.co.uk Thu Jul 15 14:40:05 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 19:40:05 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: > > Hello! > > How can I convert a SFF file from 454 into a Fastq format? > > Thanks a lot! > > JUAN I am aware of three options, none of which use Perl, (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget which), to give you FASTA+QUAL, then using your tool of choice go to FASTQ (e.g. BioPerl). (2) Use the open source command line tool sff_extract (written in Python), it can do FASTA and QUAL, and I think there is an option for FASTQ too. http://bioinf.comav.upv.es/sff_extract/ (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. Things are more complex if you are working with paired end data... Peter From cjfields at illinois.edu Thu Jul 15 15:01:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:01:32 -0500 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Jul 15, 2010, at 12:46 PM, Dan Bolser wrote: > On 15 July 2010 15:59, Dave Messina wrote: >> >>> I've put my code example with comments here: >>> >>> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair >> >> Great, thanks. Much appreciated. >> >> >>> One of the main reasons that I gave up editing the wiki is the very >>> slow response time. >> >> Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > > How big is the wiki database? > > How about moving to http://bifx.org? Depends. We have talked about migrating most (all?) of the most significantly used parts (wiki, blogs) to other sources for a while. The GitHub move also played into that. But this would be a wider OBF-based issue, as it would also involve migrating other OBF-based wikis as well. chris From cjfields at illinois.edu Thu Jul 15 15:04:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:04:15 -0500 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Jul 15, 2010, at 1:40 PM, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter We are planning some tools for SFF work with BioPerl, possibly using BioLib's io_lib bindings. Much of this is to replace the legacy io_lib bindings from bioperl-ext, which is essentially dead at the moment. chris From armendarez77 at hotmail.com Thu Jul 15 15:20:43 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Thu, 15 Jul 2010 12:20:43 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <4C3CEC50.6010102@bioperl.org> References: , <108709378.25.1279046615031.JavaMail.root@mail> , <4C3CEC50.6010102@bioperl.org> Message-ID: Thank you. I'll look into those programs. Veronica Date: Tue, 13 Jul 2010 15:44:32 -0700 From: jason at bioperl.org To: armendarez77 at hotmail.com CC: randalls at bioinfo.wsu.edu; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: That would be nice, but not possible right now :) Date: Tue, 13 Jul 2010 11:43:35 -0700 From: randalls at bioinfo.wsu.edu To: armendarez77 at hotmail.com CC: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 From cjfields at illinois.edu Fri Jul 16 00:38:10 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 23:38:10 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release Message-ID: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> All, After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? chris From dan.bolser at gmail.com Fri Jul 16 03:59:01 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 16 Jul 2010 08:59:01 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: (In theory,) the list of tools that produce and consume SFF can be found here: http://seqwiki.org/SFF Currently listed (and not already mentioned) is: * http://seqwiki.org/PyroBayes On 15 July 2010 19:40, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From chiragmatkarbioinfo at gmail.com Fri Jul 16 11:15:09 2010 From: chiragmatkarbioinfo at gmail.com (chirag matkar) Date: Fri, 16 Jul 2010 20:45:09 +0530 Subject: [Bioperl-l] Perl Web Crawling Message-ID: Hello, My Question Is not based on any Biological Application but in General How can we use Perl extensively in Web Crawling ? -- Regards, Chirag Matkar BTech Bioinformatics From cjfields at illinois.edu Fri Jul 16 11:23:01 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jul 2010 10:23:01 -0500 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <1E0BBB82-C6B4-4351-9133-7E8C4832D252@illinois.edu> http://lmgtfy.com/?q=Perl+Web+crawling chris On Jul 16, 2010, at 10:15 AM, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > > -- > Regards, > Chirag Matkar > BTech Bioinformatics > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From rmb32 at cornell.edu Fri Jul 16 11:23:04 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:04 -0700 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C407958.3010405@cornell.edu> Hi Chirag, This is off-topic for this list, it's not for general Perl questions. Search the CPAN at http://search.cpan.org, there are many modules there that can help you with this. In particular, I would look at WWW::Mechanize. Rob chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From rmb32 at cornell.edu Fri Jul 16 11:23:53 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:53 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: <4C407989.5040609@cornell.edu> My thoughts on this: It sounds like a good plan. Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. So, something to think about going forward. Rob Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From roy.chaudhuri at gmail.com Fri Jul 16 11:24:44 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Fri, 16 Jul 2010 16:24:44 +0100 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C4079BC.5010601@gmail.com> Hi Chirag, This is not an appropriate mailing list for your question, it is intended for discussion of the BioPerl toolkit, not generic bioinformatics or Perl questions. Also, before sending a question to any mailing list you should attempt to answer it yourself. Did you try typing "Perl Web Crawling" into Google? The top few hits look like they may be useful. Cheers, Roy. On 16/07/2010 16:15, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From jun.yin at ucd.ie Fri Jul 16 11:54:36 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Fri, 16 Jul 2010 16:54:36 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign Message-ID: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Dear all, I am the Google Summer of Code student working on refactoring Bio::Align subsystems. The first aim of the project is to recode Bio::SimpleAlign. This is because this package is really useful, but it was created a long time ago, written by several people, and a bit inconsistent mainly due to the above two reasons. I tried to keep the package consistent (e.g. method calling, coding styles) with the previous distribution. However, there are still a few changes. Since this package is created and used by the community, I think it is better to show it to everyone before it is merged with the major distribution. Any suggestions and criticisms are welcome. Here are the major improvements on Bio::SimpleAlign 1. MSA modifying and selection methods are more consistent and easier to use. I have enabled multiple/reverse selections for all sequences/columns selection methods, and change the names to be more understandable. For example, $aln->select() and $aln->select_noncont() are both deprecated, and renamed as $aln->select_Seqs() now. Because selections should be both in seqs and columns, which need to be explicit in the method call. For example, multiple sequence selections can be called by: $newaln=$aln->select_Seqs([4..10,20..35,37]); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37]); Or you can toggle selection(reverse selection) using: $newaln=$aln->select_Seqs([4..10,20..35,37],1); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37],-toggle=>1); If you can the method using the old ways, e.g. $newaln=$aln->select(1,5); A warning will be shown: select - deprecated method. Use select_Seqs() instead. And, the calling will be redirected to $newaln=$aln->select_Seqs([1..5]); 2. gap chars/missing chars are more consistent in the package Default values for gap char and missing char are now set in the package. Calling/Setting gap char should be made by calling $aln->gap_char("-"). 3. Some redundant methods are removed. The methods are moved to more reasonable categories. For example, $aln->select and $aln->select_noncont are deprecated now. Please use $aln->select_Seqs. 4. Some methods are renamed. Methods selecting/giving objects are capitalized, e.g. each_seq to each_Seq. Another example, the method is renamed to give a clearer information. $aln->purge is renamed into $aln->remove_redundant_Seqs $aln->splice_by_seq_pos is renamed to $aln->remove_gaps For further information, you can visit: http://spreadsheets.google.com/ccc?key=0AssLTcJFJMbXdDFfZGpJZlhidFY5blBneGdh QUZ6WFE &hl=en&authkey=CJTCw4QL Cheers, Jun Yin Ph.D. student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin From dan.bolser at gmail.com Fri Jul 16 19:15:03 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 17 Jul 2010 00:15:03 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: On 14 July 2010 11:27, Dan Bolser wrote: > Hi Jason, > > Thanks for the suggestion (see below). > > On 13 July 2010 23:48, Jason Stajich wrote: >> Dan - >> I'm not convinced that contig:example is proper type/source for the >> landmarks & scaffold - i use 'scaffold:chromosome' in my data: >> >> What happens if you change the GFF3 file line from >> ctgA example contig 1 50000 . . . Name=ctgA >> to >> ctgA chromosome scaffold 1 50000 . . . Name=ctgA >> >> >> I think this can be tweaked in the config but there may be different >> defaults for the in memory and DBI::mysql implementation. > > I found that this doesn't make any difference, however, I have found > more information about what causes the bug. > > From my previous email you see that I use bp_seqfeature_load.pl with > the "--namespace volvox" option (I should have guessed it was > something to do with this). Looking closely at the resulting tables I > see that the following tables are empty > > volvox_attribute > volvox_parent2child > volvox_feature > volvox_interval_stats > volvox_name > volvox_parent2child > > > they are not empty when created without the "--namespace x" prefix, > which is why DBI::mysql 'normally' works. > > All the other tables: > > volvox_attributelist > volvox_locationlist > volvox_meta > volvox_sequence > volvox_typelist > > > appear to be created correctly, with or without the "--namespace x" prefix. It might be worth mentioning that this issue can be 'resolved' by not using the -f (fast load) option. i.e. its the specific combination of --namespace and -f that causes the bug. http://bugzilla.open-bio.org/show_bug.cgi?id=3110 > Cheers, > Dan. > >> -jason >> Dan Bolser wrote, On 7/13/10 12:49 AM: >> >> Cheers Chris, >> >> Is there a known good version of >> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? >> I believe that this is one of the more common databases, so I'm >> surprised to find it broken. >> >> What would be the git command to roll back to a stable BioPerl / GBrowse? >> >> >> Sorry for the basic questions, >> Dan. >> >> On 12 July 2010 17:56, Chris Fields wrote: >> >> >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >> >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > From bernd.web at gmail.com Sat Jul 17 08:21:46 2010 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 17 Jul 2010 14:21:46 +0200 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: Dear Jun, Thanks for your work on this. Just a few remarks. -is changing methods names indeed needed? this will break existing code (for some time) -i am not sure how naming is generally done now in BioPerl, but is used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has an "_" followed by a capital. I'd stick with each_seq like names. You now changed it too "each_Seq" but gap_char for example remained gap_char. But surely others know better how/if to change naming. > 2. gap chars/missing chars are more consistent in the package > Default values for gap char and missing char are now set in the package. > Calling/Setting gap char should be made by calling $aln->gap_char("-"). So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char. > Another example, the method is renamed to give a clearer information. > > $aln->purge is renamed into $aln->remove_redundant_Seqs Purge to me is a clear name in aln context ;-) > $aln->splice_by_seq_pos is renamed to $aln->remove_gaps But there was already a remove_gaps method. $aln2 = $aln->remove_gaps Function : Creates an aligment with gaps removed Title : splice_by_seq_pos Usage : $status = splice_by_seq_pos(1); Function: splices all aligned sequences where the specified sequence has gaps. So remove_gaps now takes an optional argument to indicate a 'reference' sequence for splicing? Cheers, Bernd From cjfields at illinois.edu Sat Jul 17 13:07:50 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 12:07:50 -0500 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: On Jul 17, 2010, at 7:21 AM, Bernd Web wrote: > Dear Jun, > > Thanks for your work on this. > Just a few remarks. > -is changing methods names indeed needed? this will break existing > code (for some time) There is expected to be a standard deprecation cycle along with this. Changes would not be merged in until after the 1.6.2 release. > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has > an "_" followed by a capital. I'd stick with each_seq like names. You > now changed it too "each_Seq" but gap_char for example remained > gap_char. But surely others know better how/if to change naming. Technically, we would like to standardize that when object(s) are returned (such as each_seq and it's previous incarnations) the method would have the class in caps, whereas simple data would not. There have been several starts along this path, but I think various methods (next_seq in SeqIO being one) still haven't changed. Also, just to point out, it's not terribly hard to alias these as needed: *eachSeq = \&each_Seq; >> 2. gap chars/missing chars are more consistent in the package >> Default values for gap char and missing char are now set in the package. >> Calling/Setting gap char should be made by calling $aln->gap_char("-"). > So the change here is that now the default values are actually set in > new, instead of setting a the default by calling gap_char. Maybe Jun could answer this, but to me this one makes sense (methods like this, which are relied upon for various reaons, need defaults for proper state). '-' is the most commonly-used symbol. >> Another example, the method is renamed to give a clearer information. >> >> $aln->purge is renamed into $aln->remove_redundant_Seqs > Purge to me is a clear name in aln context ;-) Possibly. However alignments can hold more than sequence data (stockholm format, for example), so maybe purge() on it's own is not descriptive enough. Jun, is remove_redundant_Seqs() an alias/reimplementation for purge()? The name might be a little misleading. >> $aln->splice_by_seq_pos is renamed to $aln->remove_gaps > But there was already a remove_gaps method. > $aln2 = $aln->remove_gaps > Function : Creates an aligment with gaps removed > > Title : splice_by_seq_pos > Usage : $status = splice_by_seq_pos(1); > Function: splices all aligned sequences where the specified sequence > has gaps. > > So remove_gaps now takes an optional argument to indicate a > 'reference' sequence for splicing? > > > Cheers, > Bernd This one I'm not sure about, as the two methods to me seem unrelated from name alone. Jun? chris From cjfields at illinois.edu Sun Jul 18 00:23:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 23:23:49 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <4C407989.5040609@cornell.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> <4C407989.5040609@cornell.edu> Message-ID: On Jul 16, 2010, at 10:23 AM, Robert Buels wrote: > My thoughts on this: > > It sounds like a good plan. > > Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Precisely. > Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. > > If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. > > So, something to think about going forward. > > Rob I mentioned this at BOSC (it's briefly touched upon in the talk); it was agreed that the bottom-up approach is the best. Basically, if we can somehow emulate the larger distribution by allowing installation of the various packages then it makes life much easier for users, just have to decide what is the best approach. chris From rondonbio at yahoo.com.br Sun Jul 18 07:55:44 2010 From: rondonbio at yahoo.com.br (Rondon Neto) Date: Sun, 18 Jul 2010 04:55:44 -0700 (PDT) Subject: [Bioperl-l] Jaccard Dendrogram Message-ID: <750495.60162.qm@web63703.mail.re1.yahoo.com> Hi! Please, can I build a dendrogram from a jaccard distance matrix by Phylogenetic Analysis Pipeline? How to do that? Thank you Rondon From hlapp at drycafe.net Sun Jul 18 10:26:34 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 18 Jul 2010 10:26:34 -0400 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <89E90610-355B-4568-BFE2-301B7F4A7E61@drycafe.net> On Jul 17, 2010, at 8:21 AM, Bernd Web wrote: > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq" each_XXX is the old convention, which we aimed to deprecate before 1.4.x, in fact. Maybe we haven't swept through the entire codebase, but where we can we should certain change it. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From David.Messina at sbc.su.se Sun Jul 18 13:26:52 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 18 Jul 2010 11:26:52 -0600 Subject: [Bioperl-l] Jaccard Dendrogram In-Reply-To: <750495.60162.qm@web63703.mail.re1.yahoo.com> References: <750495.60162.qm@web63703.mail.re1.yahoo.com> Message-ID: Hi Rondon, No, I don't think BioPerl has the ability to do Jaccard distance calculations. Looks like SciPy-cluster can, though: http://code.google.com/p/scipy-cluster/ Also MATLAB probably. However, if you or anyone ese should be so inclined, it should be straightforward to adapt one of the existing BioPerl distance methods. See e.g. Bio::Align::DNAStatistics: http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html Dave On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > Hi! Please, can I build a dendrogram from a jaccard distance matrix by > Phylogenetic Analysis Pipeline? > How to do that? > > Thank you > > Rondon > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From florent.angly at gmail.com Mon Jul 19 04:47:39 2010 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 19 Jul 2010 18:47:39 +1000 Subject: [Bioperl-l] New Bio::Root::IO->_insert() method Message-ID: <4C44112B.1060701@gmail.com> Hi list, I needed a feature to insert text at an arbitrary line in a file for a Bioperl module I am working on. I coded it, called the new method _insert( ) and added it to the Bio::Root::IO module because I realized that it could be useful to other Bioperl modules. The method seems to be working well and does not cause tests to fail but let me know if you encounter issues with it. Regards, Florent From jun.yin at ucd.ie Mon Jul 19 06:43:50 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Mon, 19 Jul 2010 11:43:50 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <004c01cb272f$4626b880$d2742980$%yin@ucd.ie> Hi, Thx for all your comments. 1. About each_seq(each_Seq) As Chris Fields says, we tend to capitalize the method name which returns objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so it is better to use a capitalized name as each_Seq. But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because it may be confused with the each() function in Core. So it may need to be renamed to next_Seq eventually. Usually, what I do for the old method is: sub each_seq { my $self = shift; $self->deprecated("each_seq - deprecated method. Use each_Seq() instead."); $self->each_Seq(); } Thus, if you call the old method, it will still continue to run, but give a deprecated warning. This is done on all deprecated methods. 2. To Bernd Web, " So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char." Yes, gap_char has a default value "-" now, so is missing_char "?" and match_char ".". 3. To Bernd Web and Chris Fields, remove_redundant_Seqs() is just an alias for purge(). However, splice_by_seq_pos() is reimplemented and merged with the old remove_gaps(), because these two methods are actually doing similar things. The new remove_gaps() is: Title : remove_gaps Usage : $aln2 = $aln->remove_gaps(-reference=>5) Function : Creates an aligment with gaps removed Returns : a Bio::SimpleAlign object Args : -GAPCHAR a gap character(optional) if none specified taken from $self->gap_char, -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) indicates that only all-gaps columns should be deleted -REFERENCE splices all aligned sequences where the specified sequence has gaps. If you call the old splice_by_seq_pos(), it will be redirected to remove_gaps() by: sub splice_by_seq_pos{ my $self = shift; $self->deprecated("splice_by_seq_pos - deprecated method. Use remove_gaps() instead."); $self->remove_gaps(-reference=>$_[0]); } When I finally finish the recoding for Bio::SimpleAlign, I will write an online HOWTO. Plus, I think I will include an update log, to show which method is renamed and which is reimplemented, thus to make things clearer. Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin __________ Information from ESET Smart Security, version of virus signature database 5291 (20100719) __________ The message was checked by ESET Smart Security. http://www.eset.com From kellert at ohsu.edu Mon Jul 19 13:05:24 2010 From: kellert at ohsu.edu (Tom Keller) Date: Mon, 19 Jul 2010 10:05:24 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 20 In-Reply-To: References: Message-ID: Greetings, R has a jaccard function also. See http://pbil.univ-lyon1.fr/library/prabclus/html/jaccard.html for a description. cheers, Thomas (Tom) Keller, PhD kellert at ohsu.edu 503.494.2442 6339b R Jones Hall (BSc/CROET) www.ohsu.edu/xd/research/research-cores/dna-analysis/ On Jul 19, 2010, at 9:00 AM, wrote: > Send Bioperl-l mailing list submissions to > bioperl-l at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/bioperl-l > or, via email, send a message with subject or body 'help' to > bioperl-l-request at lists.open-bio.org > > You can reach the person managing the list at > bioperl-l-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioperl-l digest..." > > > Today's Topics: > > 1. Re: Jaccard Dendrogram (Dave Messina) > 2. New Bio::Root::IO->_insert() method (Florent Angly) > 3. Re: Recoding Bio::SimpleAlign (Jun Yin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 18 Jul 2010 11:26:52 -0600 > From: Dave Messina > Subject: Re: [Bioperl-l] Jaccard Dendrogram > To: Rondon Neto > Cc: bioperl-l at lists.open-bio.org > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Hi Rondon, > > No, I don't think BioPerl has the ability to do Jaccard distance > calculations. Looks like SciPy-cluster can, though: > > http://code.google.com/p/scipy-cluster/ > > Also MATLAB probably. > > However, if you or anyone ese should be so inclined, it should be > straightforward to adapt one of the existing BioPerl distance methods. See > e.g. Bio::Align::DNAStatistics: > > http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html > > > > > Dave > > > > > > On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > >> Hi! Please, can I build a dendrogram from a jaccard distance matrix by >> Phylogenetic Analysis Pipeline? >> How to do that? >> >> Thank you >> >> Rondon >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > ------------------------------ > > Message: 2 > Date: Mon, 19 Jul 2010 18:47:39 +1000 > From: Florent Angly > Subject: [Bioperl-l] New Bio::Root::IO->_insert() method > To: bioperl-l BioPerl > Message-ID: <4C44112B.1060701 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi list, > I needed a feature to insert text at an arbitrary line in a file for a > Bioperl module I am working on. I coded it, called the new method > _insert( ) and added it to the Bio::Root::IO module because I realized > that it could be useful to other Bioperl modules. The method seems to be > working well and does not cause tests to fail but let me know if you > encounter issues with it. > Regards, > Florent > > > ------------------------------ > > Message: 3 > Date: Mon, 19 Jul 2010 11:43:50 +0100 > From: Jun Yin > Subject: Re: [Bioperl-l] Recoding Bio::SimpleAlign > To: "'Bernd Web'" > Cc: bioperl-l at lists.open-bio.org, 'Chris Fields' > , bernd.web at gmail.com > Message-ID: <004c01cb272f$4626b880$d2742980$%yin at ucd.ie> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > Thx for all your comments. > > 1. About each_seq(each_Seq) > As Chris Fields says, we tend to capitalize the method name which returns > objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so > it is better to use a capitalized name as each_Seq. > But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because > it may be confused with the each() function in Core. So it may need to be > renamed to next_Seq eventually. > > Usually, what I do for the old method is: > > sub each_seq { > my $self = shift; > $self->deprecated("each_seq - deprecated method. Use each_Seq() > instead."); > $self->each_Seq(); > } > > Thus, if you call the old method, it will still continue to run, but give a > deprecated warning. This is done on all deprecated methods. > > > 2. To Bernd Web, " So the change here is that now the default values are > actually set in new, instead of setting a the default by calling gap_char." > > Yes, gap_char has a default value "-" now, so is missing_char "?" and > match_char ".". > > 3. To Bernd Web and Chris Fields, > remove_redundant_Seqs() is just an alias for purge(). > However, splice_by_seq_pos() is reimplemented and merged with the old > remove_gaps(), because these two methods are actually doing similar things. > The new remove_gaps() is: > > Title : remove_gaps > Usage : $aln2 = $aln->remove_gaps(-reference=>5) > Function : Creates an aligment with gaps removed > Returns : a Bio::SimpleAlign object > Args : -GAPCHAR a gap character(optional) if none specified taken > from $self->gap_char, > -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) > indicates that only all-gaps columns should be deleted > -REFERENCE splices all aligned sequences where the specified > sequence has gaps. > > If you call the old splice_by_seq_pos(), it will be redirected to > remove_gaps() by: > sub splice_by_seq_pos{ > my $self = shift; > $self->deprecated("splice_by_seq_pos - deprecated method. Use > remove_gaps() instead."); > $self->remove_gaps(-reference=>$_[0]); > } > > When I finally finish the recoding for Bio::SimpleAlign, I will write an > online HOWTO. > Plus, I think I will include an update log, to show which method is renamed > and which is reimplemented, thus to make things clearer. > > Cheers, > Jun Yin > Ph.D.?student in U.C.D. > > Bioinformatics Laboratory > Conway Institute > University College Dublin > > > > __________ Information from ESET Smart Security, version of virus signature > database 5291 (20100719) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > > > > > > ------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > End of Bioperl-l Digest, Vol 87, Issue 20 > ***************************************** From jonathan at leto.net Mon Jul 19 18:59:27 2010 From: jonathan at leto.net (Jonathan Leto) Date: Mon, 19 Jul 2010 15:59:27 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: Howdy, I recently found a bug in parsing InterPro XML, which I have created a bug for, as well as patches which fix the problem with a test case: http://bugzilla.open-bio.org/show_bug.cgi?id=3121 I would very much like to get feedback on this patch and have it included in the next 1.6.x release. Thanks, Duke On Thu, Jul 15, 2010 at 9:38 PM, Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. ?This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. ?That will be followed by releases of the run, db, and network distributions. ?Any other thoughts? ?Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jonathan "Duke" Leto jonathan at leto.net http://leto.net From jay at jays.net Mon Jul 19 18:24:05 2010 From: jay at jays.net (Jay Hannah) Date: Mon, 19 Jul 2010 17:24:05 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <9331AD17-C3FB-47E9-80C3-2D1360E9EC8C@jays.net> Greetings, I opened bug 3120 today. Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? http://bugzilla.open-bio.org/show_bug.cgi?id=3120 http://bugzilla.open-bio.org/attachment.cgi?id=1526 Or maybe it's just me? :) Thanks, Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From ycchen1981 at gmail.com Mon Jul 19 23:47:45 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Tue, 20 Jul 2010 11:47:45 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.abi format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my $in = Bio::SeqIO->new(-file => "$inputfilename", -format => 'abi'); my $out = Bio::SeqIO->new(-file => ">$outputfilename", -format => 'phd'); while ( my $seq = $in->next_seq() ) { for my $curr(1 .. $seq->length()) { print "[",$seq->qualat($curr),"]:"; print "[",$seq->trace_index_at($curr),"]\t"; } $out->write_seq($seq); last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From Jonathan_Epstein at nih.gov Tue Jul 20 13:53:00 2010 From: Jonathan_Epstein at nih.gov (Jonathan Epstein) Date: Tue, 20 Jul 2010 13:53:00 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? Message-ID: <4C45E27C.9090400@nih.gov> Hi, I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. Then there's the small matter of loading the hg18 annotations into the appropriate relational database. Thanks in advance for your guidance, Jonathan From rmb32 at cornell.edu Tue Jul 20 14:42:36 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 20 Jul 2010 11:42:36 -0700 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <4C45EE1C.7080401@cornell.edu> Take a look at Bio::DB::SeqFeature::Store. It's got a loader that ships with bioperl, bp_seqfeature_load.pl. perldoc Bio::DB::SeqFeature::Store. From the sound of it, the GMOD/Chado stuff might be too heavyweight for what you are doing. But a good method for accessing a Chado schema from Perl is Bio::Chado::Schema, http://search.cpan.org/perldoc?Bio::Chado::Schema, which is based on DBIx::Class. Hope this helps! Rob Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features > associated with a particular genomic region in the hg18 human assembly. > This seems to require a relational database. Of course I would like to > do this using Bioperl. > > So then the question becomes: what's the best approach to use? > Biosql/BioPerl-db looks like the cleanest solution, but it's not clear > to me how up-to-date it is; it sort of looks like an abandoned project. > > CHADO/Gmod is more actively maintained, but I don't know how/whether I > can obtain BioPerl bindings. > > I am also open to using the UCSC databases as a starting point, since > I've already mirrored most of the human-related portions of the UCSC > environment. > > > Then there's the small matter of loading the hg18 annotations into the > appropriate relational database. > > > Thanks in advance for your guidance, > > Jonathan > > > > > > _______________________________________________ > 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 Jul 20 14:55:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jul 2010 13:55:15 -0500 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <827D02E9-9AA8-4474-BBA4-FC15BAAC49F4@illinois.edu> On Jul 20, 2010, at 12:53 PM, Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. > > So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. Not really abandoned, but it won't help in this case unless you intend on converting to BioSQL. > CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. Look at Bio::Schema:Chado. It's more middleware, no direct BioPerl bindings yet. > I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. > > Then there's the small matter of loading the hg18 annotations into the appropriate relational database. > > Thanks in advance for your guidance, > > Jonathan Bio::DB::SeqFeature::Store. Export the data into GTF; I think the database will load this (via Bio::DB::SeqFeature::Store::GFF2Loader). Otherwise, using the ensembl perl API is an option. One can install the database locally and use the Ensembl Perl API to extract the information you need. There were modules that were intended as interfaces to the remote UCSC databases but (IIRC) there was significant concern from the UCSC folks about overloading the UCSC server with queries, so they were basically deprecated (were only partially developed anyway). chris From hlapp at drycafe.net Tue Jul 20 15:40:10 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 20 Jul 2010 15:40:10 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <0369BC4D-9769-47AE-AF6C-B43BAAEC2327@drycafe.net> On Jul 20, 2010, at 1:53 PM, Jonathan Epstein wrote: > Biosql/BioPerl-db looks like the cleanest solution, but it's not > clear to me how up-to-date it is; it sort of looks like an abandoned > project. It's not abandoned at all. I'm not sure though it serves your use-case - it sounds like some GFF store would meet your needs much better. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From florent.angly at gmail.com Tue Jul 20 18:05:22 2010 From: florent.angly at gmail.com (Florent Angly) Date: Wed, 21 Jul 2010 08:05:22 +1000 Subject: [Bioperl-l] Fwd: gene extraction script Message-ID: <4C461DA2.5090009@gmail.com> -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ From awitney at sgul.ac.uk Wed Jul 21 04:02:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 09:02:01 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <84B8D550-E4CA-4027-99A8-D05F1B5E8DEE@sgul.ac.uk> Hi Nicholas, If you just want to retrieve sequences from GenBank, try this: http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl HTH adam On 20 Jul 2010, at 23:05, Florent Angly wrote: > > > -------- Original Message -------- > Subject: gene extraction script > Date: Tue, 20 Jul 2010 15:56:36 +0100 > From: Nicholas Brown > To: > > > > Hi, > > Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? > Thanks so much for your time in reading this. > > Kind Regards, > > Nicholas Brown > > Script > http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl > #!/usr/bin/perl -w > # $Id$ > =pod > > > =head1 NAME > > > extract_genes.pl - extract genomic sequences from NCBI files > using BioPerl > > > =head1 DESCRIPTION > > > This script is a simple solution to the problem of > extracting genomic regions corresponding to genes. There are other > solutions, this particular approach uses genomic sequence > files from NCBI and gene coordinates from Entrez Gene. > > > The first time this script is run it will be slow as it will > extract species-specific data from the gene2accession file and create > a storable hash (retrieving the positional data from this hash is > significantly faster than reading gene2accession each time the script > runs). The subsequent runs should be fast. > > > =head1 INSTALLATION > > > =head2 > > > Install BioPerl, full instructions at http://bioperl.org. > > > =head2 Download gene2accession.gz > > > Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into > your working directory and gunzip it. > > > =head2 Download sequence files > > > Create one or more species directories in the working directory, the > directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). > > > Download the nucleotide fasta files for a given species from its CHR* > directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a > species directory. The sequence files will have the suffix ".fna" or > "fa.gz", gunzip if necessary. > > > =head2 Determine Taxon id > > > Determine the taxon id for the given species. This id is the first column > in the gene2accession file. Modify the %species hash in this script > such that name of your species directory is a key and the taxon id is the > value. > > > =head2 Command-line options > > > -i Gene id > -s Name of species directory > -h Help > > > Example: > > > extract_genes.pl -i 850302 -s Sc > > > =cut > > > use strict; > use Bio::DB::Fasta; > use Getopt::Long; > use Storable; > > my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae > "Ec" => 83333, # Escherichia coli K12 > "Hs" => 9606 # H. sapiens > ); > > my ($help,$id,$name); > > GetOptions( "s=s" => \$name, > "i=i" => \$id, > "h" => \$help ); > > usage() if ($help || !$id || !$name); > > my $storedHash = $name . ".dump"; > > # create index for a directory of fasta files > my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); > > # extract species-specific data from gene2accession > unless (-e $storedHash) { > my $ref; > # extract species-specific information from gene2accession > open MYIN,"gene2accession" or die "No gene2accession file\n"; > while () { > my @arr = split "\t",$_; > if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { > ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, > $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = > ($arr[9], $arr[10], $arr[11], $arr[7]); > } > } > # save species-specific information using Storable > store $ref, $storedHash; > } > > # retrieve the species-specific data from a stored hash > my $ref = retrieve($storedHash); > > # retrieve sequence and sub-sequence > if (defined $ref->{$id}) { > my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); > my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); > $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); > > # Insert SeqIO options here... > print $seq->seq,"\n"; > } else { > print "Cannot find id: $id\n"; > } > > sub make_my_id { > my $line = shift; > $line =~ /ref\|([^|]+)/; > $1; > } > > sub usage { > system "perldoc $0"; > exit; > } > > __END__ > > > _______________________________________________ > 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 Jul 21 05:43:35 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 10:43:35 +0100 Subject: [Bioperl-l] Fwd: Fwd: gene extraction script References: <4C46B84C.4000702@univ-montp2.fr> Message-ID: forwarding to the original poster and the list... Begin forwarded message: > From: Laurent MANCHON > Date: 21 July 2010 10:05:16 GMT+01:00 > To: Adam Witney > Subject: Re: [Bioperl-l] Fwd: gene extraction script > Reply-To: lmanchon at univ-montp2.fr > > another program you can use. > > > #!/usr/bin/perl > # retrieve sequences from genbank > # read list of GenBank access number from a file and write to output.txt file > > use LWP::UserAgent; > use Bio::SeqIO; > use Bio::DB::GenBank; > $cpt=0; > $outfile = "outfile.txt"; > chomp($outfile); > $gb = new Bio::DB::GenBank; > while (<>) { > ($Fld1) = split(' ', $_, 9999); > $out = Bio::SeqIO->new('-file' => ">>$outfile",'-format' => 'fasta'); > $acc = $Fld1; > $cpt++; > print $acc,"\t$cpt"," retrieved\n"; > $seqio = $gb->get_Stream_by_acc([$acc]); > while( $seq = $seqio->next_seq() ) { > open(LOG,">>$outfile"); > printf LOG '%s ', ">" . $acc; > $out->write_seq($seq); > close(LOG); > } > > > > > > Adam Witney a ?crit : >> >> Hi Nicholas, >> >> If you just want to retrieve sequences from GenBank, try this: >> >> http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl >> >> HTH >> >> adam >> >> >> On 20 Jul 2010, at 23:05, Florent Angly wrote: >> >> >>> -------- Original Message -------- >>> Subject: gene extraction script >>> Date: Tue, 20 Jul 2010 15:56:36 +0100 >>> From: Nicholas Brown >>> To: >>> >>> >>> >>> Hi, >>> >>> Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? >>> Thanks so much for your time in reading this. >>> >>> Kind Regards, >>> >>> Nicholas Brown >>> >>> Script >>> http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl >>> #!/usr/bin/perl -w >>> # $Id$ >>> =pod >>> >>> >>> =head1 NAME >>> >>> >>> extract_genes.pl - extract genomic sequences from NCBI files >>> using BioPerl >>> >>> >>> =head1 DESCRIPTION >>> >>> >>> This script is a simple solution to the problem of >>> extracting genomic regions corresponding to genes. There are other >>> solutions, this particular approach uses genomic sequence >>> files from NCBI and gene coordinates from Entrez Gene. >>> >>> >>> The first time this script is run it will be slow as it will >>> extract species-specific data from the gene2accession file and create >>> a storable hash (retrieving the positional data from this hash is >>> significantly faster than reading gene2accession each time the script >>> runs). The subsequent runs should be fast. >>> >>> >>> =head1 INSTALLATION >>> >>> >>> =head2 >>> >>> >>> Install BioPerl, full instructions at http://bioperl.org. >>> >>> >>> =head2 Download gene2accession.gz >>> >>> >>> Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into >>> your working directory and gunzip it. >>> >>> >>> =head2 Download sequence files >>> >>> >>> Create one or more species directories in the working directory, the >>> directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). >>> >>> >>> Download the nucleotide fasta files for a given species from its CHR* >>> directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a >>> species directory. The sequence files will have the suffix ".fna" or >>> "fa.gz", gunzip if necessary. >>> >>> >>> =head2 Determine Taxon id >>> >>> >>> Determine the taxon id for the given species. This id is the first column >>> in the gene2accession file. Modify the %species hash in this script >>> such that name of your species directory is a key and the taxon id is the >>> value. >>> >>> >>> =head2 Command-line options >>> >>> >>> -i Gene id >>> -s Name of species directory >>> -h Help >>> >>> >>> Example: >>> >>> >>> extract_genes.pl -i 850302 -s Sc >>> >>> >>> =cut >>> >>> >>> use strict; >>> use Bio::DB::Fasta; >>> use Getopt::Long; >>> use Storable; >>> >>> my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae >>> "Ec" => 83333, # Escherichia coli K12 >>> "Hs" => 9606 # H. sapiens >>> ); >>> >>> my ($help,$id,$name); >>> >>> GetOptions( "s=s" => \$name, >>> "i=i" => \$id, >>> "h" => \$help ); >>> >>> usage() if ($help || !$id || !$name); >>> >>> my $storedHash = $name . ".dump"; >>> >>> # create index for a directory of fasta files >>> my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); >>> >>> # extract species-specific data from gene2accession >>> unless (-e $storedHash) { >>> my $ref; >>> # extract species-specific information from gene2accession >>> open MYIN,"gene2accession" or die "No gene2accession file\n"; >>> while () { >>> my @arr = split "\t",$_; >>> if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { >>> ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, >>> $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = >>> ($arr[9], $arr[10], $arr[11], $arr[7]); >>> } >>> } >>> # save species-specific information using Storable >>> store $ref, $storedHash; >>> } >>> >>> # retrieve the species-specific data from a stored hash >>> my $ref = retrieve($storedHash); >>> >>> # retrieve sequence and sub-sequence >>> if (defined $ref->{$id}) { >>> my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); >>> my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); >>> $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); >>> >>> # Insert SeqIO options here... >>> print $seq->seq,"\n"; >>> } else { >>> print "Cannot find id: $id\n"; >>> } >>> >>> sub make_my_id { >>> my $line = shift; >>> $line =~ /ref\|([^|]+)/; >>> $1; >>> } >>> >>> sub usage { >>> system "perldoc $0"; >>> exit; >>> } >>> >>> __END__ >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 jun.yin at ucd.ie Wed Jul 21 06:32:25 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Wed, 21 Jul 2010 11:32:25 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <012201cb28c0$027eb000$077c1000$%yin@ucd.ie> Hi, Nicolas, You don't need to edit the original code. Usually the package developed by the community provides enough methods for you. You may consider to use the recent developed package Bio::DB::EUtilities to retrieve the sequences from GenBank. See HOWTO here: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Florent Angly Sent: Tuesday, July 20, 2010 11:05 PM To: bioperl-l List; n.brown at nhm.ac.uk Subject: [Bioperl-l] Fwd: gene extraction script -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_ge nes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com From amritavisdom at gmail.com Sat Jul 17 07:21:27 2010 From: amritavisdom at gmail.com (AMRITA VISDOM) Date: Sat, 17 Jul 2010 16:51:27 +0530 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita From ycchen1981 at gmail.com Mon Jul 19 03:11:39 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Mon, 19 Jul 2010 15:11:39 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my ?$in ?= Bio::SeqIO->new(-file => "$inputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'abi'); my ?$out = Bio::SeqIO->new(-file => ">$outputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'phd'); while ( my $seq = $in->next_seq() ) { ? ? ? for my $curr(1 .. ?$seq->length()) { ? ? ? ? ? ? ? print "[",$seq->qualat($curr),"]:"; ? ? ? ? ? ? ? print "[",$seq->trace_index_at($curr),"]\t"; ? ? ? } ? ? ? $out->write_seq($seq); ? ? ? last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From amritavisdom at gmail.com Mon Jul 19 07:25:19 2010 From: amritavisdom at gmail.com (Amritavisdom) Date: Mon, 19 Jul 2010 04:25:19 -0700 (PDT) Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: <29203643.post@talk.nabble.com> Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita -- View this message in context: http://old.nabble.com/Parsing-Alternative-Splicing-Gene-information-from-Genbank-file-using-Bioperl-tp29203643p29203643.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From gabriel.jabud at gmail.com Tue Jul 20 14:36:54 2010 From: gabriel.jabud at gmail.com (Gabriel Ab) Date: Tue, 20 Jul 2010 11:36:54 -0700 (PDT) Subject: [Bioperl-l] Finding mutations in Blast files Message-ID: <29216321.post@talk.nabble.com> I'm trying to write a script to find mutations in a Blast output file. The result should look something like [A/G] (query/subject) for SNPs and [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if possible. I was able to get both the query and subject sequence extracted from blast files, but parsing through that for mutations without the help of modules and writing them like above is harder than it sounds. Deletions and other things in the alignment can make it very tricky. I tried looking for modules that would make this task easier but I couldn't find anything. Can someone point me in the right direction on how to do this or let me know about modules that could help? Thanks. -- View this message in context: http://old.nabble.com/Finding-mutations-in-Blast-files-tp29216321p29216321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From taw-bioperl at dowfamily.net Tue Jul 20 19:46:05 2010 From: taw-bioperl at dowfamily.net (Ycart) Date: Tue, 20 Jul 2010 23:46:05 +0000 (UTC) Subject: [Bioperl-l] Accessing karyotype data from Ensembl Message-ID: Hi, I am trying to figure out the correct syntax to access the karyotype data from the Ensembl database. I need to use the start and end base pair coordinates for the karyotype bands in a separate program, which means I need to be able to use that data, not just view it. I'm thinking that it will be like getting slices as described in the Core API Tutorial, but with some other word than 'Slice' in: my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); Any ideas on how to do this under the current API? -Tracy From cjfields at illinois.edu Wed Jul 21 17:43:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 16:43:32 -0500 Subject: [Bioperl-l] Accessing karyotype data from Ensembl In-Reply-To: References: Message-ID: You should contact the ensembl mail list for ensembl-related questions; this lies outside the bioperl domain. chris On Jul 20, 2010, at 6:46 PM, Ycart wrote: > Hi, > > I am trying to figure out the correct syntax to access the karyotype data from > the Ensembl database. I need to use the start and end base pair coordinates for > the karyotype bands in a separate program, which means I need to be able to use > that data, not just view it. > > I'm thinking that it will be like getting slices as described in the Core API > Tutorial, but with some other word than 'Slice' in: > my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); > > > Any ideas on how to do this under the current API? > > > -Tracy > > _______________________________________________ > 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 Jul 21 18:04:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 17:04:48 -0500 Subject: [Bioperl-l] Finding mutations in Blast files In-Reply-To: <29216321.post@talk.nabble.com> References: <29216321.post@talk.nabble.com> Message-ID: <1B5D46EC-BC67-43BB-9376-4A246CB093AD@illinois.edu> On Jul 20, 2010, at 1:36 PM, Gabriel Ab wrote: > > I'm trying to write a script to find mutations in a Blast output file. > The result should look something like [A/G] (query/subject) for SNPs and > [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if > possible. In order to get upstream and downstream you will need access to the original sequence (this information is not reported in the BLAST file). Use the HSP coords to pull that information. > I was able to get both the query and subject sequence extracted from blast > files, but parsing through that for mutations without the help of modules > and writing them like above is harder than it sounds. Deletions and other > things in the alignment can make it very tricky. I tried looking for > modules that would make this task easier but I couldn't find anything. ... > Can someone point me in the right direction on how to do this or let me know > about modules that could help? > > Thanks Bio::Search::HSP::GenericHSP::seq_inds() does something along these lines, e.g. iterates through the two strings by index position and stores relevant information. In this case, you would just print out [X/Y] where there is no match, or [--/XY] when gaps are present. Look at the code for that method to get the general idea. chris From David.Messina at sbc.su.se Wed Jul 21 18:43:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 21 Jul 2010 16:43:07 -0600 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl In-Reply-To: <29203643.post@talk.nabble.com> References: <29203643.post@talk.nabble.com> Message-ID: Hi Amrita, You will want to read the Feature Annotation HOWTO for details of how to parse a Genbank file: http://www.bioperl.org/wiki/HOWTO:Feature-Annotation Dave From cjfields at illinois.edu Wed Jul 21 20:09:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 19:09:05 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: Message-ID: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> It's very possible this is due to API changes within io_lib, but I can't be sure. Aaron, any idea? Just to note, we no longer recommend using the bioperl-ext modules, mainly b/c they have not been actively maintained, so much so that updating them to use the current API is quite difficult (might involve some extensive refactoring). The BioLib project, however, has perl bindings to io_lib. If one had time they could incorporate the BioLib io_lib bindings into bioperl, but I believe ABI support was removed a while ago so that will be problematic. chris On Jul 19, 2010, at 2:11 AM, ??? wrote: > Hi, > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > bioperl-ext-1.5.1, and io-lib-1.8.11; > my OS was 32-bit, Centos 5.2. > When I convert abi-format files to phd-format files, > the value of quality of all bases are '0', and the value of > trace_index of all bases are undefined. > Is there any possible reason leading to this problem? > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > 0.980904.e in phd files; > if this is the case, where can I find phred executers? > > The following is the code utilizing BioPerl and results from BioPerl > and Phred respectively: > ============================================== > #!/usr/bin/perl -w > unshift(@INC, "/opt/BioPerl-1.6.1/"); > unshift(@INC, "/opt/bioperl-ext"); > use strict; > use Bio::SeqIO; > > my $inputfilename='./HMA040184H12.T3.ab1'; > my $outputfilename='test11.phd'; > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > -format => 'abi'); > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > -format => 'phd'); > > while ( my $seq = $in->next_seq() ) { > for my $curr(1 .. $seq->length()) { > print "[",$seq->qualat($curr),"]:"; > print "[",$seq->trace_index_at($curr),"]\t"; > } > $out->write_seq($seq); > last; > } > > ================== test11.phd (by Bio::SeqIO) ================= > BEGIN_SEQUENCE (null) > > BEGIN_COMMENT > > CHROMAT_FILE: unknown > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.980904.e > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Mon Jul 19 11:59:09 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: unknown > CHEM: unknown > DYE: unknown > > END_COMMENT > > BEGIN_DNA > A 0 > G 0 > G 0 > G 0 > G 0 > . > . > . > . > > G 0 > T 0 > T 0 > G 0 > T 0 > C 0 > G 0 > C 0 > T 0 > A 0 > C 0 > END_DNA > > END_SEQUENCE > > ================== .phd (by phred 0.020425.c) ======================= > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > BEGIN_COMMENT > > CHROMAT_FILE: HMA040184H12.T3.ab1 > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.020425.c > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Fri Jul 9 16:20:59 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: 11905 > TRIM: 38 900 0.0500 > TRACE_PEAK_AREA_RATIO: 0.0630 > CHEM: term > DYE: big > > END_COMMENT > > BEGIN_DNA > a 11 2 > g 11 13 > g 11 22 > a 11 37 > a 11 52 > g 8 65 > c 6 76 > t 6 91 > c 6 97 > . > . > . > a 14 11840 > c 16 11849 > a 16 11861 > a 12 11873 > c 12 11885 > g 12 11897 > END_DNA > > END_SEQUENCE > ================================================ > Sincerely yours, > Yen-Chang Chen > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From amackey at virginia.edu Wed Jul 21 20:36:02 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Wed, 21 Jul 2010 20:36:02 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the bioperl-ext modules are not installed? Regardless, can you get a dump of the $seq objects before you hand them off to Bio::SeqIO::phd -- have the qual scores already been lost (problem with the abi reader), or not (problem with the phd writer)? And a basic question -- I assume your .abi files actually have quality values in them (not all do)? -Aaron On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > It's very possible this is due to API changes within io_lib, but I can't be > sure. Aaron, any idea? > > Just to note, we no longer recommend using the bioperl-ext modules, mainly > b/c they have not been actively maintained, so much so that updating them to > use the current API is quite difficult (might involve some extensive > refactoring). The BioLib project, however, has perl bindings to io_lib. If > one had time they could incorporate the BioLib io_lib bindings into bioperl, > but I believe ABI support was removed a while ago so that will be > problematic. > > chris > > On Jul 19, 2010, at 2:11 AM, ??? wrote: > > > Hi, > > > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > > bioperl-ext-1.5.1, and io-lib-1.8.11; > > my OS was 32-bit, Centos 5.2. > > When I convert abi-format files to phd-format files, > > the value of quality of all bases are '0', and the value of > > trace_index of all bases are undefined. > > Is there any possible reason leading to this problem? > > > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > > 0.980904.e in phd files; > > if this is the case, where can I find phred executers? > > > > The following is the code utilizing BioPerl and results from BioPerl > > and Phred respectively: > > ============================================== > > #!/usr/bin/perl -w > > unshift(@INC, "/opt/BioPerl-1.6.1/"); > > unshift(@INC, "/opt/bioperl-ext"); > > use strict; > > use Bio::SeqIO; > > > > my $inputfilename='./HMA040184H12.T3.ab1'; > > my $outputfilename='test11.phd'; > > > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > > -format => 'abi'); > > > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > > -format => 'phd'); > > > > while ( my $seq = $in->next_seq() ) { > > for my $curr(1 .. $seq->length()) { > > print "[",$seq->qualat($curr),"]:"; > > print "[",$seq->trace_index_at($curr),"]\t"; > > } > > $out->write_seq($seq); > > last; > > } > > > > ================== test11.phd (by Bio::SeqIO) ================= > > BEGIN_SEQUENCE (null) > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: unknown > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.980904.e > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Mon Jul 19 11:59:09 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: unknown > > CHEM: unknown > > DYE: unknown > > > > END_COMMENT > > > > BEGIN_DNA > > A 0 > > G 0 > > G 0 > > G 0 > > G 0 > > . > > . > > . > > . > > > > G 0 > > T 0 > > T 0 > > G 0 > > T 0 > > C 0 > > G 0 > > C 0 > > T 0 > > A 0 > > C 0 > > END_DNA > > > > END_SEQUENCE > > > > ================== .phd (by phred 0.020425.c) ======================= > > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: HMA040184H12.T3.ab1 > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.020425.c > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Fri Jul 9 16:20:59 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: 11905 > > TRIM: 38 900 0.0500 > > TRACE_PEAK_AREA_RATIO: 0.0630 > > CHEM: term > > DYE: big > > > > END_COMMENT > > > > BEGIN_DNA > > a 11 2 > > g 11 13 > > g 11 22 > > a 11 37 > > a 11 52 > > g 8 65 > > c 6 76 > > t 6 91 > > c 6 97 > > . > > . > > . > > a 14 11840 > > c 16 11849 > > a 16 11861 > > a 12 11873 > > c 12 11885 > > g 12 11897 > > END_DNA > > > > END_SEQUENCE > > ================================================ > > Sincerely yours, > > Yen-Chang Chen > > > > _______________________________________________ > > 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 Jul 21 22:41:16 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 21:41:16 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Nope; doesn't appear to be a pure-perl parser for this. Was there one? chris On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > bioperl-ext modules are not installed? > > Regardless, can you get a dump of the $seq objects before you hand them off > to Bio::SeqIO::phd -- have the qual scores already been lost (problem with > the abi reader), or not (problem with the phd writer)? > > And a basic question -- I assume your .abi files actually have quality > values in them (not all do)? > > -Aaron > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > >> It's very possible this is due to API changes within io_lib, but I can't be >> sure. Aaron, any idea? >> >> Just to note, we no longer recommend using the bioperl-ext modules, mainly >> b/c they have not been actively maintained, so much so that updating them to >> use the current API is quite difficult (might involve some extensive >> refactoring). The BioLib project, however, has perl bindings to io_lib. If >> one had time they could incorporate the BioLib io_lib bindings into bioperl, >> but I believe ABI support was removed a while ago so that will be >> problematic. >> >> chris >> >> On Jul 19, 2010, at 2:11 AM, ??? wrote: >> >>> Hi, >>> >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, >>> bioperl-ext-1.5.1, and io-lib-1.8.11; >>> my OS was 32-bit, Centos 5.2. >>> When I convert abi-format files to phd-format files, >>> the value of quality of all bases are '0', and the value of >>> trace_index of all bases are undefined. >>> Is there any possible reason leading to this problem? >>> >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is >>> 0.980904.e in phd files; >>> if this is the case, where can I find phred executers? >>> >>> The following is the code utilizing BioPerl and results from BioPerl >>> and Phred respectively: >>> ============================================== >>> #!/usr/bin/perl -w >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); >>> unshift(@INC, "/opt/bioperl-ext"); >>> use strict; >>> use Bio::SeqIO; >>> >>> my $inputfilename='./HMA040184H12.T3.ab1'; >>> my $outputfilename='test11.phd'; >>> >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", >>> -format => 'abi'); >>> >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", >>> -format => 'phd'); >>> >>> while ( my $seq = $in->next_seq() ) { >>> for my $curr(1 .. $seq->length()) { >>> print "[",$seq->qualat($curr),"]:"; >>> print "[",$seq->trace_index_at($curr),"]\t"; >>> } >>> $out->write_seq($seq); >>> last; >>> } >>> >>> ================== test11.phd (by Bio::SeqIO) ================= >>> BEGIN_SEQUENCE (null) >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: unknown >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.980904.e >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Mon Jul 19 11:59:09 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: unknown >>> CHEM: unknown >>> DYE: unknown >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> A 0 >>> G 0 >>> G 0 >>> G 0 >>> G 0 >>> . >>> . >>> . >>> . >>> >>> G 0 >>> T 0 >>> T 0 >>> G 0 >>> T 0 >>> C 0 >>> G 0 >>> C 0 >>> T 0 >>> A 0 >>> C 0 >>> END_DNA >>> >>> END_SEQUENCE >>> >>> ================== .phd (by phred 0.020425.c) ======================= >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: HMA040184H12.T3.ab1 >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.020425.c >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Fri Jul 9 16:20:59 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: 11905 >>> TRIM: 38 900 0.0500 >>> TRACE_PEAK_AREA_RATIO: 0.0630 >>> CHEM: term >>> DYE: big >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> a 11 2 >>> g 11 13 >>> g 11 22 >>> a 11 37 >>> a 11 52 >>> g 8 65 >>> c 6 76 >>> t 6 91 >>> c 6 97 >>> . >>> . >>> . >>> a 14 11840 >>> c 16 11849 >>> a 16 11861 >>> a 12 11873 >>> c 12 11885 >>> g 12 11897 >>> END_DNA >>> >>> END_SEQUENCE >>> ================================================ >>> Sincerely yours, >>> Yen-Chang Chen >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 alperyilmaz at gmail.com Thu Jul 22 00:09:38 2010 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Thu, 22 Jul 2010 00:09:38 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO Message-ID: Hi, I was using Bio::SeqIO with perl one-liner and I noticed an oddity. Can someone suggest a correction or workaround? Let test.fa be; >1 AGTC >2 CTGA Then, commandline below prints the expected output: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < test.fa output: 1 AGTC 2 CTGA However, if use the command in a pipe, then the output has an issue with primary_id of initial sequence. $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' output: AGTC 2 CTGA What is the workaround to make Bio::SeqIO work correctly in a one-liner with pipes? thanks, Alper Yilmaz Post-doctoral Researcher Plant Biotechnology Center The Ohio State University 1060 Carmack Rd Columbus, OH 43210 (614)688-4954 PS: Normally, the example is demonstrating useless use of cat, for the sake giving an example, it can be "command1 | command2 | command3 | perl -MBioSeqIO -e'...' " instead.. From fs5 at sanger.ac.uk Thu Jul 22 06:48:25 2010 From: fs5 at sanger.ac.uk (Frank Schwach) Date: Thu, 22 Jul 2010 11:48:25 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: Message-ID: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Hi Alper, You can actually reproduce it also by providing STDIN from keyboard input like so: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >1 aaaaaaaaa >2 aaaaaaaaa ggggggggg >3 2 ggggggggg ccccccccc 3 ccccccccc In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} then the command returned the sequence of the first entry without the ID again. >From the second entry onwards, it is all correct. I'm not 100% sure but could it be linked to buffering? SeqIO has to read ahead to find a complete entry that spans multiple lines. When you get STDIN from a file, you will get buffering and receive more than one line at once, which will allow the next_seq method to work as expected. If you provide line-by-line input then that method probably can't work correctly. If that is the case then you can't use the command in a pipe at all. Frank On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: > Hi, > > I was using Bio::SeqIO with perl one-liner and I noticed an oddity. > Can someone suggest a correction or workaround? > > Let test.fa be; > >1 > AGTC > >2 > CTGA > > Then, commandline below prints the expected output: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < > test.fa > > output: > 1 AGTC > 2 CTGA > > However, if use the command in a pipe, then the output has an issue > with primary_id of initial sequence. > $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > =>\*STDIN); while ($myseq=$seq->next_seq){ print > $myseq->id,"\t",$myseq->seq,"\n"}' > > output: > AGTC > 2 CTGA > > What is the workaround to make Bio::SeqIO work correctly in a > one-liner with pipes? > > thanks, > > Alper Yilmaz > Post-doctoral Researcher > Plant Biotechnology Center > The Ohio State University > 1060 Carmack Rd > Columbus, OH 43210 > (614)688-4954 > > > PS: Normally, the example is demonstrating useless use of cat, for the > sake giving an example, it can be "command1 | command2 | command3 | > perl -MBioSeqIO -e'...' " instead.. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- 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 roy.chaudhuri at gmail.com Thu Jul 22 07:49:41 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 12:49:41 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Message-ID: <4C483055.5050402@gmail.com> Hi Alper, The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. Cheers. Roy. On 22/07/2010 11:48, Frank Schwach wrote: > Hi Alper, > > You can actually reproduce it also by providing STDIN from keyboard > input like so: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >> 1 > aaaaaaaaa >> 2 > aaaaaaaaa > ggggggggg >> 3 > 2 ggggggggg > ccccccccc > 3 ccccccccc > > In this case I typed > ">1"[ENTER] > "aaaaaaaaa"[ENTER] > ">2"[ENTER} > then the command returned the sequence of the first entry without the ID > again. >> From the second entry onwards, it is all correct. > > I'm not 100% sure but could it be linked to buffering? SeqIO has to read > ahead to find a complete entry that spans multiple lines. When you get > STDIN from a file, you will get buffering and receive more than one line > at once, which will allow the next_seq method to work as expected. If > you provide line-by-line input then that method probably can't work > correctly. > If that is the case then you can't use the command in a pipe at all. > > Frank > > > > On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >> Hi, >> >> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >> Can someone suggest a correction or workaround? >> >> Let test.fa be; >>> 1 >> AGTC >>> 2 >> CTGA >> >> Then, commandline below prints the expected output: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >> test.fa >> >> output: >> 1 AGTC >> 2 CTGA >> >> However, if use the command in a pipe, then the output has an issue >> with primary_id of initial sequence. >> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> $myseq->id,"\t",$myseq->seq,"\n"}' >> >> output: >> AGTC >> 2 CTGA >> >> What is the workaround to make Bio::SeqIO work correctly in a >> one-liner with pipes? >> >> thanks, >> >> Alper Yilmaz >> Post-doctoral Researcher >> Plant Biotechnology Center >> The Ohio State University >> 1060 Carmack Rd >> Columbus, OH 43210 >> (614)688-4954 >> >> >> PS: Normally, the example is demonstrating useless use of cat, for the >> sake giving an example, it can be "command1 | command2 | command3 | >> perl -MBioSeqIO -e'...' " instead.. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From amackey at virginia.edu Thu Jul 22 09:19:52 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 09:19:52 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Message-ID: Hmm, perhaps I'm thinking about the SCF code, not the ABI code. -Aaron On Wed, Jul 21, 2010 at 10:41 PM, Chris Fields wrote: > Nope; doesn't appear to be a pure-perl parser for this. Was there one? > > chris > > On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > > > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > > bioperl-ext modules are not installed? > > > > Regardless, can you get a dump of the $seq objects before you hand them > off > > to Bio::SeqIO::phd -- have the qual scores already been lost (problem > with > > the abi reader), or not (problem with the phd writer)? > > > > And a basic question -- I assume your .abi files actually have quality > > values in them (not all do)? > > > > -Aaron > > > > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields > wrote: > > > >> It's very possible this is due to API changes within io_lib, but I can't > be > >> sure. Aaron, any idea? > >> > >> Just to note, we no longer recommend using the bioperl-ext modules, > mainly > >> b/c they have not been actively maintained, so much so that updating > them to > >> use the current API is quite difficult (might involve some extensive > >> refactoring). The BioLib project, however, has perl bindings to io_lib. > If > >> one had time they could incorporate the BioLib io_lib bindings into > bioperl, > >> but I believe ABI support was removed a while ago so that will be > >> problematic. > >> > >> chris > >> > >> On Jul 19, 2010, at 2:11 AM, ??? wrote: > >> > >>> Hi, > >>> > >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > >>> bioperl-ext-1.5.1, and io-lib-1.8.11; > >>> my OS was 32-bit, Centos 5.2. > >>> When I convert abi-format files to phd-format files, > >>> the value of quality of all bases are '0', and the value of > >>> trace_index of all bases are undefined. > >>> Is there any possible reason leading to this problem? > >>> > >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > >>> 0.980904.e in phd files; > >>> if this is the case, where can I find phred executers? > >>> > >>> The following is the code utilizing BioPerl and results from BioPerl > >>> and Phred respectively: > >>> ============================================== > >>> #!/usr/bin/perl -w > >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); > >>> unshift(@INC, "/opt/bioperl-ext"); > >>> use strict; > >>> use Bio::SeqIO; > >>> > >>> my $inputfilename='./HMA040184H12.T3.ab1'; > >>> my $outputfilename='test11.phd'; > >>> > >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", > >>> -format => 'abi'); > >>> > >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", > >>> -format => 'phd'); > >>> > >>> while ( my $seq = $in->next_seq() ) { > >>> for my $curr(1 .. $seq->length()) { > >>> print "[",$seq->qualat($curr),"]:"; > >>> print "[",$seq->trace_index_at($curr),"]\t"; > >>> } > >>> $out->write_seq($seq); > >>> last; > >>> } > >>> > >>> ================== test11.phd (by Bio::SeqIO) ================= > >>> BEGIN_SEQUENCE (null) > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: unknown > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.980904.e > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Mon Jul 19 11:59:09 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: unknown > >>> CHEM: unknown > >>> DYE: unknown > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> A 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> . > >>> . > >>> . > >>> . > >>> > >>> G 0 > >>> T 0 > >>> T 0 > >>> G 0 > >>> T 0 > >>> C 0 > >>> G 0 > >>> C 0 > >>> T 0 > >>> A 0 > >>> C 0 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> > >>> ================== .phd (by phred 0.020425.c) ======================= > >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: HMA040184H12.T3.ab1 > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.020425.c > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Fri Jul 9 16:20:59 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: 11905 > >>> TRIM: 38 900 0.0500 > >>> TRACE_PEAK_AREA_RATIO: 0.0630 > >>> CHEM: term > >>> DYE: big > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> a 11 2 > >>> g 11 13 > >>> g 11 22 > >>> a 11 37 > >>> a 11 52 > >>> g 8 65 > >>> c 6 76 > >>> t 6 91 > >>> c 6 97 > >>> . > >>> . > >>> . > >>> a 14 11840 > >>> c 16 11849 > >>> a 16 11861 > >>> a 12 11873 > >>> c 12 11885 > >>> g 12 11897 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> ================================================ > >>> Sincerely yours, > >>> Yen-Chang Chen > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/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 Jul 22 09:27:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 08:27:30 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C483055.5050402@gmail.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> Message-ID: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Would someone like to file this as a bug? My guess is this may be a combination of using pipes and the way FASTA is parsed (locally resets $/). http://bugzilla.open-bio.org chris On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > Hi Alper, > > The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. > > Cheers. > Roy. > > On 22/07/2010 11:48, Frank Schwach wrote: >> Hi Alper, >> >> You can actually reproduce it also by providing STDIN from keyboard >> input like so: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >>> 1 >> aaaaaaaaa >>> 2 >> aaaaaaaaa >> ggggggggg >>> 3 >> 2 ggggggggg >> ccccccccc >> 3 ccccccccc >> >> In this case I typed >> ">1"[ENTER] >> "aaaaaaaaa"[ENTER] >> ">2"[ENTER} >> then the command returned the sequence of the first entry without the ID >> again. >>> From the second entry onwards, it is all correct. >> >> I'm not 100% sure but could it be linked to buffering? SeqIO has to read >> ahead to find a complete entry that spans multiple lines. When you get >> STDIN from a file, you will get buffering and receive more than one line >> at once, which will allow the next_seq method to work as expected. If >> you provide line-by-line input then that method probably can't work >> correctly. >> If that is the case then you can't use the command in a pipe at all. >> >> Frank >> >> >> >> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>> Hi, >>> >>> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >>> Can someone suggest a correction or workaround? >>> >>> Let test.fa be; >>>> 1 >>> AGTC >>>> 2 >>> CTGA >>> >>> Then, commandline below prints the expected output: >>> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >>> test.fa >>> >>> output: >>> 1 AGTC >>> 2 CTGA >>> >>> However, if use the command in a pipe, then the output has an issue >>> with primary_id of initial sequence. >>> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>> >>> output: >>> AGTC >>> 2 CTGA >>> >>> What is the workaround to make Bio::SeqIO work correctly in a >>> one-liner with pipes? >>> >>> thanks, >>> >>> Alper Yilmaz >>> Post-doctoral Researcher >>> Plant Biotechnology Center >>> The Ohio State University >>> 1060 Carmack Rd >>> Columbus, OH 43210 >>> (614)688-4954 >>> >>> >>> PS: Normally, the example is demonstrating useless use of cat, for the >>> sake giving an example, it can be "command1 | command2 | command3 | >>> perl -MBioSeqIO -e'...' " instead.. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 roy.chaudhuri at gmail.com Thu Jul 22 09:41:00 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 14:41:00 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C484A6C.1000502@gmail.com> Done (bug 3122). On 22/07/2010 14:27, Chris Fields wrote: > Would someone like to file this as a bug? My guess is this may be a > combination of using pipes and the way FASTA is parsed (locally > resets $/). > > http://bugzilla.open-bio.org > > chris > > On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > >> Hi Alper, >> >> The problem comes about because you don't specify -format=>'fasta' >> in your Bio::SeqIO object. BioPerl attempts to guess the format if >> you don't specify it, but seems to be struggling in this case. I >> can't really think of any good reason for not specifying the >> format. Just in case anyone wants to investigate further, I noticed >> that if you try the example with longer fasta sequences, the first >> line of the sequence is interpreted as the id, with the remainder >> as the sequence. >> >> Cheers. Roy. >> >> On 22/07/2010 11:48, Frank Schwach wrote: >>> Hi Alper, >>> >>> You can actually reproduce it also by providing STDIN from >>> keyboard input like so: $ perl -MBio::SeqIO -e 'my >>> $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> 1 >>> aaaaaaaaa >>>> 2 >>> aaaaaaaaa ggggggggg >>>> 3 >>> 2 ggggggggg ccccccccc 3 ccccccccc >>> >>> In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} >>> then the command returned the sequence of the first entry without >>> the ID again. >>>> From the second entry onwards, it is all correct. >>> >>> I'm not 100% sure but could it be linked to buffering? SeqIO has >>> to read ahead to find a complete entry that spans multiple lines. >>> When you get STDIN from a file, you will get buffering and >>> receive more than one line at once, which will allow the next_seq >>> method to work as expected. If you provide line-by-line input >>> then that method probably can't work correctly. If that is the >>> case then you can't use the command in a pipe at all. >>> >>> Frank >>> >>> >>> >>> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>>> Hi, >>>> >>>> I was using Bio::SeqIO with perl one-liner and I noticed an >>>> oddity. Can someone suggest a correction or workaround? >>>> >>>> Let test.fa be; >>>>> 1 >>>> AGTC >>>>> 2 >>>> CTGA >>>> >>>> Then, commandline below prints the expected output: $ perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}'< test.fa >>>> >>>> output: 1 AGTC 2 CTGA >>>> >>>> However, if use the command in a pipe, then the output has an >>>> issue with primary_id of initial sequence. $ cat test.fa | perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> >>>> output: AGTC 2 CTGA >>>> >>>> What is the workaround to make Bio::SeqIO work correctly in a >>>> one-liner with pipes? >>>> >>>> thanks, >>>> >>>> Alper Yilmaz Post-doctoral Researcher Plant Biotechnology >>>> Center The Ohio State University 1060 Carmack Rd Columbus, OH >>>> 43210 (614)688-4954 >>>> >>>> >>>> PS: Normally, the example is demonstrating useless use of cat, >>>> for the sake giving an example, it can be "command1 | command2 >>>> | command3 | perl -MBioSeqIO -e'...' " instead.. >>>> _______________________________________________ Bioperl-l >>>> mailing list Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 sheetu.piscean at gmail.com Wed Jul 21 17:49:25 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Wed, 21 Jul 2010 14:49:25 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Adding some more details on OS and BioPerl version OS: sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 UTC 2010 i686 GNU/Linux Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi BioPerl Version : sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' 1.006001 Attached is the error that I get while running the RemoteBlast. Thanks, Sheetal On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani wrote: > Hi, > > I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > is the complete script : > #Remote-blast "factory object" creation and blast-parameter > initialization > > use Bio::Tools::Run::RemoteBlast; > use strict; > my $prog = 'blastx'; > my $db = 'nr/nt'; > my $e_val= '1e-10'; > > my @params = ( '-prog' => $prog, > '-data' => $db, > '-expect' => $e_val, > '-readmethod' => 'SearchIO' ); > > my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > #$v is just to turn on and off the messages > my $v = 0; > > my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > ); > > while (my $input = $str->next_seq()){ > #Blast a sequence against a database: > > #Alternatively, you could pass in a file with many > #sequences rather than loop through sequence one at a time > #Remove the loop starting 'while (my $input = $str->next_seq())' > #and swap the two lines below for an example of that. > my $r = $factory->submit_blast($input); > #my $r = $factory->submit_blast('amino.fa'); > > print STDERR "waiting..." if( $v > 0 ); > while ( my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = $factory->retrieve_blast($rid); > if( !ref($rc) ) { > if( $rc < 0 ) { > print "removing rid as rc is < 0"; > $factory->remove_rid($rid); > } > print STDERR "." if ( $v > 0 ); > sleep 5; > } else { > my $result = $rc->next_result(); > #save the output > print "saving to file"; > my $filename = "contig_236.out"; #$result->query_name()."\.out"; > $factory->save_output($filename); > $factory->remove_rid($rid); > print "\nQuery Name: ", $result->query_name(), "\n"; > while ( my $hit = $result->next_hit ) { > next unless ( $v > 0); > print "\thit name is ", $hit->name, "\n"; > while( my $hsp = $hit->next_hsp ) { > print "\t\tscore is ", $hsp->score, "\n"; > } > } > } > } > } > } > > But when I run this, I get an error in html format which says "Cannot > accept request, error code: -103". Attaching the error file for reference. > Can you please help me with debugging this error? Your help is much > appreciated. > > Also, informing about the previous error that I fixed by adding this line: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > I was getting prior to adding this line was : > --------------------- WARNING --------------------- > MSG:

An error has occurred on the > server, The server is unable to format right now, please try again in a few > minutes. If the problem (Informational Message: No alias or index file > found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4CF5MY9101P

> > It kinda took me a while to find out the 2 requirements > > # 1) set your database like this: > -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > > # 2) add this line before submitting the job: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > I think it will be great if you can add this to the synopsis section of > RemoteBlast.pm > > Thanks, > Sheetal > -------------- next part -------------- An HTML attachment was scrubbed... URL: From evelyne.c88 at gmail.com Thu Jul 22 09:57:47 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 06:57:47 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> Message-ID: <29237193.post@talk.nabble.com> Hi, I would like to run a SW alignment, but i'm new to programming... Tried using several tutorials to install this Bioperl-ext package, but not getting that far... Maybe you can help? -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29237193.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From biopython at maubp.freeserve.co.uk Thu Jul 22 10:41:21 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 15:41:21 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29237193.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: > > Hi, > > I would like to run a SW alignment, but i'm new to programming... > Tried using several tutorials to install this Bioperl-ext package, but not > getting that far... > Maybe you can help? How about using the water tool in EMBOSS? I'm sure BioPerl has wrappers for that... http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html Peter From cjfields at illinois.edu Thu Jul 22 11:31:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 10:31:30 -0500 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Jul 22, 2010, at 9:41 AM, Peter wrote: > On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: >> >> Hi, >> >> I would like to run a SW alignment, but i'm new to programming... >> Tried using several tutorials to install this Bioperl-ext package, but not >> getting that far... >> Maybe you can help? > > How about using the water tool in EMBOSS? I'm sure BioPerl has > wrappers for that... > > http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html > > Peter Yes, we do. I would suggest that solution as well; the SW work in bioperl-ext hasn't been maintained actively for a while. That doesn't mean it won't suit your needs, but issues with compilation will likely remained unaddressed. chris From evelyne.c88 at gmail.com Thu Jul 22 10:09:30 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 07:09:30 -0700 (PDT) Subject: [Bioperl-l] installing Bioperl-ext package (Bio::Tools::pSW) Message-ID: <29237314.post@talk.nabble.com> Hi I'm kind of a rookie at programming, but i'm trying to align two sequences. And i would like to use Bio::Tools::pSW I have followed instructions and installed a C compiler (devC++) I read a lot of different tutorials, but cannot find a way to install this package, everything i try gives errors latest error when i tried 'install B/BIRNEY/bioperl-ext-1.4.tar.gz' : c:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site' returned status 512, won't make running make test make had some problems, won't test running make install make had some problems, won't install -- View this message in context: http://old.nabble.com/installing-Bioperl-ext-package-%28Bio%3A%3ATools%3A%3ApSW%29-tp29237314p29237314.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From evelyne.c88 at gmail.com Thu Jul 22 11:21:17 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:21:17 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: <29238161.post@talk.nabble.com> I have really no idea what that means... Studying first year of bio-informatics, and have to make a small perl program as exam Maybe I'm in a bit over my head, I'll ask the tutor for some advice... < References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C4855EE.1010208@bms.com> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm if (defined $self->{-file}) { # Close the file we opened. close($fh); } elsif (ref $fh eq 'GLOB') { # Try seeking to the start position. >>> seek($fh, $start_pos, 0); } elsif (defined $fh && $fh->can('setpos')) { # Seek to the start position. $fh->setpos($start_pos); } return ($done ? $fmt_string : undef); seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset is where the second non-null line starts. I am not sure why- all manuals claim this should work? Hope this helps. Stefan On 7/22/2010 9:27 AM, Chris Fields wrote: > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From biopython at maubp.freeserve.co.uk Thu Jul 22 11:42:25 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 16:42:25 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29238161.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: > > I have really no idea what that means... > Studying first year of bio-informatics, and have to make a small perl > program as exam > Maybe I'm in a bit over my head, I'll ask the tutor for some advice... > The EMBOSS project is a collection of open source command line tools written in C, and includes a tool called "water" for doing Smith Waterman (SW) sequence alignments. I was suggesting you could use BioPerl to call this needle program and parse its output. However, it sounds like you actually have a programming assignment where the point is to actually implement the SW algorithm yourself (in perl). In this case, EMBOSS won't be useful after all. Peter From evelyne.c88 at gmail.com Thu Jul 22 11:53:39 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:53:39 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: <29238557.post@talk.nabble.com> There is actually no real assignment with a goal described. We only have to prove that we understand and can use Perl. (Description of the course states we are to learn the concepts of computer programming, and rudimentary Perl) The Smith Waterman Tool was mentioned during the courses (along with BPlite, and using remote and local BLASTs) so i wanted to explore this, without really knowing how complicated the use of this could be... Maybe they just wanted to let us know what possibilities there are, without expecting that we could do this on our own... Peter-329 wrote: > > On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: >> >> I have really no idea what that means... >> Studying first year of bio-informatics, and have to make a small perl >> program as exam >> Maybe I'm in a bit over my head, I'll ask the tutor for some advice... >> > > The EMBOSS project is a collection of open source command line > tools written in C, and includes a tool called "water" for doing Smith > Waterman (SW) sequence alignments. I was suggesting you could > use BioPerl to call this needle program and parse its output. > > However, it sounds like you actually have a programming assignment > where the point is to actually implement the SW algorithm yourself (in > perl). In this case, EMBOSS won't be useful after all. > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29238557.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From amackey at virginia.edu Thu Jul 22 13:15:18 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 13:15:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C4855EE.1010208@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. -Aaron On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov wrote: > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset > is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> > > > _______________________________________________ > 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 Jul 22 14:35:51 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 13:35:51 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C48853F.3050904@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): tell() on pipes, fifos, and sockets usually returns -1. My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: if (!$self->seekable) { #die a horrible death } chris On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). > I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) > I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. > Another option is to right to a temp file or slurp into memory. This could be dangerous though... > > On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >> >> -Aaron >> >> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: >> >> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >> >> if (defined $self->{-file}) { >> # Close the file we opened. >> close($fh); >> } elsif (ref $fh eq 'GLOB') { >> # Try seeking to the start position. >> >>> seek($fh, $start_pos, 0); >> } elsif (defined $fh && $fh->can('setpos')) { >> # Seek to the start position. >> $fh->setpos($start_pos); >> } >> return ($done ? $fmt_string : undef); >> >> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >> after reset is where the second non-null line starts. >> I am not sure why- all manuals claim this should work? >> Hope this helps. >> Stefan >> >> On 7/22/2010 9:27 AM, Chris Fields wrote: >> >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > From dunlopjp.ctr at afrl.hpc.mil Thu Jul 22 12:35:01 2010 From: dunlopjp.ctr at afrl.hpc.mil (Mr. James P. Dunlop (Contractor)) Date: Thu, 22 Jul 2010 12:35:01 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org Message-ID: <4C487335.4080808@afrl.hpc.mil> Hello I very new to this type of install. I am trying to install this as non root, which may be part of the problem, but I thought I found some information that addresses this. Also I'm trying to use cpan. The error before termination is: Files=44, Tests=1140, 30 wallclock secs (22.97 cusr + 6.94 csys = 29.91 CPU) /usr/bin/make test -- OK Running make install /usr/bin/perl Build --makefile_env_macros 1 install Building Module-Build Writing /app/bioperl/BioPerl-1.6.0/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Module/Build/.packlist /usr/bin/make install -- OK Couldn't install Module::Build, giving up. Running make test Make had some problems, maybe interrupted? Won't test Running make install Make had some problems, maybe interrupted? Won't install cpan> Is there anything that is obvious to you folks? Would it be possible to cc any e-mails to dunlopjp at aol.com? Thanks Jim Dunlop 937-255-0050 From stefan.kirov at bms.com Thu Jul 22 13:51:59 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 13:51:59 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: <4C48853F.3050904@bms.com> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. Another option is to right to a temp file or slurp into memory. This could be dangerous though... On 7/22/2010 1:15 PM, Aaron Mackey wrote: > You cannot seek on a pipe, unfortunately. SeqIO should probably try > to detect this, and die rather than invoking GuessSeqFormat. > > -Aaron > > On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: > > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh > after reset is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From stefan.kirov at bms.com Thu Jul 22 15:37:18 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 15:37:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: <4C489DEE.1010806@bms.com> Chris, I tested tell and for me it actually returns the correct position. I think seek($fh, $start_pos, 0) || $self->throw("Failed resetting the filehandle pointer; IO error occurred"); might be better. On 7/22/2010 2:35 PM, Chris Fields wrote: > It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): > > tell() on pipes, fifos, and sockets usually returns -1. > > My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: > > if (!$self->seekable) { > #die a horrible death > } > > chris > > On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > > >> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). >> I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) >> I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. >> Another option is to right to a temp file or slurp into memory. This could be dangerous though... >> >> On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> >>> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >>> >>> -Aaron >>> >>> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov> wrote: >>> >>> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >>> >>> if (defined $self->{-file}) { >>> # Close the file we opened. >>> close($fh); >>> } elsif (ref $fh eq 'GLOB') { >>> # Try seeking to the start position. >>> >>> seek($fh, $start_pos, 0); >>> } elsif (defined $fh&& $fh->can('setpos')) { >>> # Seek to the start position. >>> $fh->setpos($start_pos); >>> } >>> return ($done ? $fmt_string : undef); >>> >>> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >>> after reset is where the second non-null line starts. >>> I am not sure why- all manuals claim this should work? >>> Hope this helps. >>> Stefan >>> >>> On 7/22/2010 9:27 AM, Chris Fields wrote: >>> >>> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> >>> $myseq->id,"\t",$myseq->seq,"\n"} >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >> >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From cjfields at illinois.edu Thu Jul 22 19:54:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 18:54:20 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? chris On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > Adding some more details on OS and BioPerl version > > OS: > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > UTC 2010 i686 GNU/Linux > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > BioPerl Version : > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > 'print $Bio::Root::Version::VERSION,"\n"' > 1.006001 > > Attached is the error that I get while running the RemoteBlast. > > Thanks, > Sheetal > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > wrote: > >> Hi, >> >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here >> is the complete script : >> #Remote-blast "factory object" creation and blast-parameter >> initialization >> >> use Bio::Tools::Run::RemoteBlast; >> use strict; >> my $prog = 'blastx'; >> my $db = 'nr/nt'; >> my $e_val= '1e-10'; >> >> my @params = ( '-prog' => $prog, >> '-data' => $db, >> '-expect' => $e_val, >> '-readmethod' => 'SearchIO' ); >> >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); >> >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; >> >> #$v is just to turn on and off the messages >> my $v = 0; >> >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' >> ); >> >> while (my $input = $str->next_seq()){ >> #Blast a sequence against a database: >> >> #Alternatively, you could pass in a file with many >> #sequences rather than loop through sequence one at a time >> #Remove the loop starting 'while (my $input = $str->next_seq())' >> #and swap the two lines below for an example of that. >> my $r = $factory->submit_blast($input); >> #my $r = $factory->submit_blast('amino.fa'); >> >> print STDERR "waiting..." if( $v > 0 ); >> while ( my @rids = $factory->each_rid ) { >> foreach my $rid ( @rids ) { >> my $rc = $factory->retrieve_blast($rid); >> if( !ref($rc) ) { >> if( $rc < 0 ) { >> print "removing rid as rc is < 0"; >> $factory->remove_rid($rid); >> } >> print STDERR "." if ( $v > 0 ); >> sleep 5; >> } else { >> my $result = $rc->next_result(); >> #save the output >> print "saving to file"; >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; >> $factory->save_output($filename); >> $factory->remove_rid($rid); >> print "\nQuery Name: ", $result->query_name(), "\n"; >> while ( my $hit = $result->next_hit ) { >> next unless ( $v > 0); >> print "\thit name is ", $hit->name, "\n"; >> while( my $hsp = $hit->next_hsp ) { >> print "\t\tscore is ", $hsp->score, "\n"; >> } >> } >> } >> } >> } >> } >> >> But when I run this, I get an error in html format which says "Cannot >> accept request, error code: -103". Attaching the error file for reference. >> Can you please help me with debugging this error? Your help is much >> appreciated. >> >> Also, informing about the previous error that I fixed by adding this line: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that >> I was getting prior to adding this line was : >> --------------------- WARNING --------------------- >> MSG:

An error has occurred on the >> server, The server is unable to format right now, please try again in a few >> minutes. If the problem (Informational Message: No alias or index file >> found for protein database [nr/nt] in search path >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: >> 4CF5MY9101P

>> >> It kinda took me a while to find out the 2 requirements >> >> # 1) set your database like this: >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options >> >> >> # 2) add this line before submitting the job: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; >> >> I think it will be great if you can add this to the synopsis section of >> RemoteBlast.pm >> >> Thanks, >> Sheetal >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Thu Jul 22 19:52:19 2010 From: genehack at genehack.org (John Anderson) Date: Thu, 22 Jul 2010 19:52:19 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: <4C487335.4080808@afrl.hpc.mil> References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: The one thing that sticks out is this: > Couldn't install Module::Build, giving up. Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. chrs, john. From cjfields at illinois.edu Thu Jul 22 21:53:36 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:53:36 -0500 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 6:52 PM, John Anderson wrote: > > On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: > > The one thing that sticks out is this: > >> Couldn't install Module::Build, giving up. > > Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. > > chrs, > john. Also helps to set any CPAN configuration to install locally. http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA chris From cjfields at illinois.edu Thu Jul 22 21:52:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:52:15 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Removing this line from your original script worked for me: $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; This is set via '-prog' parameter. chris On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". > > Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : > An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > Adding below the email conversation with blast-help for debugging further : > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: > Sheetal, > > You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. > > Best regards, > Wayne > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. > > The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. > > Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. > > Thanks, > Sheetal > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: > Hello, > > Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > Best regards, > Wayne > > _~___~___~__~__~_~ > Wayne Matten, PhD > NCBI Public Services > mattenw at mail.nih.gov > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > Hello, > > I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : > Cannot accept request, error code: -103 > > The request that I send is : > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx >> >> Can you please help me debug it. >> >> Thanks and Regards, >> Sheetal > > Thanks > Sheetal > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sheetu.piscean at gmail.com Thu Jul 22 20:30:24 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Thu, 22 Jul 2010 17:30:24 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. Adding below the email conversation with blast-help for debugging further : On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: Sheetal, You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. Best regards, Wayne http://www.ncbi.nlm.nih.gov/blast /Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. Thanks, Sheetal On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: Hello, Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo Best regards, Wayne _~___~___~__~__~_~ Wayne Matten, PhD NCBI Public Services mattenw at mail.nih.gov On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: Hello, I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : Cannot accept request, error code: -103 The request that I send is : POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx Can you please help me debug it. Thanks and Regards, Sheetal Thanks Sheetal On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version > -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for > reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this > line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a > few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From shachigahoimbi at gmail.com Fri Jul 23 07:01:01 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:31:01 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From shachigahoimbi at gmail.com Fri Jul 23 07:28:05 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:58:05 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From giles.weaver at bbsrc.ac.uk Fri Jul 23 07:31:11 2010 From: giles.weaver at bbsrc.ac.uk (Giles Weaver) Date: Fri, 23 Jul 2010 12:31:11 +0100 Subject: [Bioperl-l] bioperl modules In-Reply-To: References: Message-ID: <4C497D7F.1060806@bbsrc.ac.uk> See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. Regards, Giles On 23/07/10 12:01, Shachi Gahoi wrote: > I want to use following bioperl modules. I have installed bioperl 1.6.I. > have searched all modules in it but i have not found following modules. I > want to use it. please tell me if anyone know about these modules and use of > it. > > temp- for temperature checking > ac- for count of AC content > gc- for count of GC content > dimer- check bases for dimerization > check 5- Check the presence of GC, CG, C or G at 5' > check 3- Check the presence of GC, CG, C or G at 3' > basepair- calculate % of GC > hairpin- calculate hairpin structure > delta- calculate delta G value for primer > temp diff- check for temperature difference in left and right primer > > please tell me if anyone know about these modules. > > Thanks in advance > > > From cjfields at illinois.edu Fri Jul 23 09:17:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 08:17:41 -0500 Subject: [Bioperl-l] bioperl modules In-Reply-To: <4C497D7F.1060806@bbsrc.ac.uk> References: <4C497D7F.1060806@bbsrc.ac.uk> Message-ID: <688164AF-AF7B-49D0-9E68-A4916C7A2DDC@illinois.edu> This sounds suspiciously like homework, so I'm reluctant to give any direct answers. Most (all?) of these are covered in the Tisdall books, IIRC, and all use regexes or transliteration, that's about all I'll say. chris On Jul 23, 2010, at 6:31 AM, Giles Weaver wrote: > See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. > Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. > > Regards, > > Giles > > On 23/07/10 12:01, Shachi Gahoi wrote: >> I want to use following bioperl modules. I have installed bioperl 1.6.I. >> have searched all modules in it but i have not found following modules. I >> want to use it. please tell me if anyone know about these modules and use of >> it. >> >> temp- for temperature checking >> ac- for count of AC content >> gc- for count of GC content >> dimer- check bases for dimerization >> check 5- Check the presence of GC, CG, C or G at 5' >> check 3- Check the presence of GC, CG, C or G at 3' >> basepair- calculate % of GC >> hairpin- calculate hairpin structure >> delta- calculate delta G value for primer >> temp diff- check for temperature difference in left and right primer >> >> please tell me if anyone know about these modules. >> >> Thanks in advance >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From pg4 at sanger.ac.uk Fri Jul 23 04:06:38 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 09:06:38 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' Message-ID: Hello, Regarding the recent post about installing bioperl as non root, http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique http://perl.jonallen.info/writing/articles/install-perl-modules-without-root I wanted to put it in the talk page first, but there is an 'issue': The talk link points to http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix Talk:Installing Bioperl for Unix 2 and in this talk page, the page link point to a deleted page http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 Editing Installing Bioperl for Unix 2 Warning: You are recreating a page that was previously deleted. You should consider whether it is appropriate to continue editing this page. The deletion log for this page is provided here for convenience: * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing Bioperl for Unix 2" ? (testing out page (adding back from file)) Just to let you know. ----- Pablo Marin-Garcia -- 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 Fri Jul 23 11:07:23 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 10:07:23 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: Message-ID: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Pablo, No idea how that happened, but I removed the older discussion page and my obsolete comment, along with the redirect on the main discussion page. Edit away! chris On Jul 23, 2010, at 3:06 AM, Pablo Marin-Garcia wrote: > Hello, > > Regarding the recent post about installing bioperl as non root, > > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. > > http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique > http://perl.jonallen.info/writing/articles/install-perl-modules-without-root > > I wanted to put it in the talk page first, but there is an 'issue': > > The talk link points to > http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix > Talk:Installing Bioperl for Unix 2 > > and in this talk page, the page link point to a deleted page > http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 > > Editing Installing Bioperl for Unix 2 > Warning: You are recreating a page that was previously deleted. > > You should consider whether it is appropriate to continue editing this page. > The deletion log for this page is provided here for convenience: > > * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing > Bioperl > for Unix 2" ? (testing out page (adding back from file)) > > > Just to let you know. > > ----- > > Pablo Marin-Garcia > > > > -- > 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. > _______________________________________________ > 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 Fri Jul 23 11:42:09 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 09:42:09 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: Thanks for that addition to the wiki, Pablo! Much appreciated. I did not know about local::lib. Dave From pg4 at sanger.ac.uk Fri Jul 23 12:52:03 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 17:52:03 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Dave Messina wrote: > Thanks for that addition to the wiki, Pablo! Much appreciated. > > I did not know about local::lib. > [This is a bit off-topic but probably useful for core developers] Then probably you don't know about App::perlbrew Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ---- Copied from the SYNOPSIS: # Initialize perlbrew init # Install some Perls perlbrew install perl-5.8.1 perlbrew install perl-5.11.5 # See what were installed perlbrew installed # Switch perl in the $PATH perlbrew switch perl-5.11.5 perl -v # Switch to another version perlbrew switch perl-5.8.1 perl -v # Switch to a certain perl executable not managed by perlbrew. perlbrew switch /usr/bin/perl # Or turn it off completely. Useful when you messed up too deep. perlbrew off # Use 'switch' command to turn it back on. perlbrew switch perl-5.11.5 -Pablo > > Dave > ----- Pablo Marin-Garcia -- 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 Fri Jul 23 12:57:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 11:57:05 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ... yes, just started using this myself. Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. chris From cjfields at illinois.edu Fri Jul 23 13:01:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:01:20 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ...and completely forgot to mention the tremendous benefits of App::perlbrew for development! Lots of very nice tools becoming available these days... chris From cjfields at illinois.edu Fri Jul 23 13:20:44 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:20:44 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> http://github.com/cjfields/bioperl6 http://github.com/cjfields/biome :) chris On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > > extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: > > http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html > > I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. > > > Have a good weekend > > -Pablo > > > > On Fri, 23 Jul 2010, Chris Fields wrote: > >> >> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >> >>> On Fri, 23 Jul 2010, Dave Messina wrote: >>> >>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>> >>>> I did not know about local::lib. >>>> >>> >>> [This is a bit off-topic but probably useful for core developers] >>> Then probably you don't know about >>> >>> App::perlbrew >>> >>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >> ... >> >> yes, just started using this myself. >> >> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >> >> chris > > > ----- > > Pablo Marin-Garcia > > > > -- > 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 sheetu.piscean at gmail.com Fri Jul 23 13:04:59 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 10:04:59 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: I did remove that line but doesn't help. I still keep getting this error: MSG:

An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4KJE1YJ601N

Any pointers ?? - Sheetal On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > This is set via '-prog' parameter. > > chris > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to Blast-help as well > and they have to say that "there is something wrong with the URL, didn't > give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default it is set to > plain, I guess this value is for standard blast pgm. like blastp, blastx, > etc) gives me this error : > > An error has occurred on the server, The server is unable to format right > now, please try again in a few minutes. If the problem (Informational > Message: No alias or index file found for protein database [nr/nt] in search > path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for debugging further > : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some errors. The > URL below works; note that order of parameters does not matter. > > > > Best regards, > > Wayne > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning immediately after > "QUERY=", (called as bare sequence) but still I get the same error. > > > > The documentation on your URLAPI says that Query can have Accession(s), > gi(S) or FASTA sequence. The format of the query for FASTA sequence is as > shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA > sequence, the query has description/definition followed by actual sequence. > In that case, the format of my POST request match the requirement. > > > > Can you help me figure out why am I still getting error : "Cannot accept > request, error code: -103" ? Attaching the log file having Query as bare > sequence and FASTA sequence for your reference. Your help is much > appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not use, requires > that the sequence begin immediately after "QUERY=". Your example shows a > definition line preceding the sequence. You can get documentation on our > URLAPI on this page (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my Bioperl script > remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded > DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 > 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a time > > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; > #$result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which says "Cannot > > >> accept request, error code: -103". Attaching the error file for > reference. > > >> Can you please help me with debugging this error? Your help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by adding this > line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has occurred on > the > > >> server, The server is unable to format right now, please try again in > a few > > >> minutes. If the problem (Informational Message: No alias or index > file > > >> found for protein database [nr/nt] in search path > > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the synopsis section > of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > From pg4 at sanger.ac.uk Fri Jul 23 13:17:50 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:17:50 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. Have a good weekend -Pablo On Fri, 23 Jul 2010, Chris Fields wrote: > > On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > >> On Fri, 23 Jul 2010, Dave Messina wrote: >> >>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>> >>> I did not know about local::lib. >>> >> >> [This is a bit off-topic but probably useful for core developers] >> Then probably you don't know about >> >> App::perlbrew >> >> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. > ... > > yes, just started using this myself. > > Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. > > chris ----- Pablo Marin-Garcia -- 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 Fri Jul 23 13:36:40 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:36:40 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> I've attached the code and example data that worked. This is using the latest bioperl on github, so maybe it's the version you have installed? chris On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > I did remove that line but doesn't help. I still keep getting this > error: > MSG:

An error has occurred on > the server, The server is unable to format right now, please try again > in a few minutes. If the problem (Informational Message: No alias or > index file found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4KJE1YJ601N

> > Any pointers ?? > > - Sheetal > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > This is set via '-prog' parameter. > > chris > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to > Blast-help as well and they have to say that "there is > something wrong with the URL, didn't give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default > it is set to plain, I guess this value is for standard blast > pgm. like blastp, blastx, etc) gives me this error : > > An error has occurred on the server, The server is unable to > format right now, please try again in a few minutes. If the > problem (Informational Message: No alias or index file found > for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for > debugging further : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some > errors. The URL below works; note that order of parameters > does not matter. > > > > Best regards, > > Wayne > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > 3EContig_236+%0A% > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning > immediately after "QUERY=", (called as bare sequence) but > still I get the same error. > > > > The documentation on your URLAPI says that Query can have > Accession(s), gi(S) or FASTA sequence. The format of the query > for FASTA sequence is as shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > for FASTA sequence, the query has description/definition > followed by actual sequence. In that case, the format of my > POST request match the requirement. > > > > Can you help me figure out why am I still getting error : > "Cannot accept request, error code: -103" ? Attaching the log > file having Query as bare sequence and FASTA sequence for your > reference. Your help is much appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not > use, requires that the sequence begin immediately after > "QUERY=". Your example shows a definition line preceding the > sequence. You can get documentation on our URLAPI on this page > (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my > Bioperl script remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > 3EContig_236+% > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI > server, not problems with the script. Is this still > occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > Jun 11 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the > RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on > 'nr' database. Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and > blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > -format => 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a > time > > >> #Remove the loop starting 'while (my $input = > $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; # > $result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), > "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which > says "Cannot > > >> accept request, error code: -103". Attaching the error > file for reference. > > >> Can you please help me with debugging this error? Your > help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by > adding this line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; The error that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has > occurred on the > > >> server, The server is unable to format right now, please > try again in a few > > >> minutes. If the problem (Informational Message: No > alias or index file > > >> found for protein database [nr/nt] in search path > > >> > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 > requirements > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the > synopsis section of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: test.pl Type: application/x-perl Size: 2211 bytes Desc: not available URL: -------------- next part -------------- >Foo My description here AATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGG CGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGA GGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCT CCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCC ACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAG AAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCAT GGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAAT GCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCC TGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCG GGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGA TTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGC CCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAG CCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAAT CCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGG CTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTAT ACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCT CAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGC GCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACG CAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTG TCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTC AGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGAT GAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTG CGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCAC GCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGA GACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACT CAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCA TCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAAC AGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAG CGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTT CTGT From pg4 at sanger.ac.uk Fri Jul 23 13:33:10 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:33:10 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Chris Fields wrote: > http://github.com/cjfields/bioperl6 oh, very nice!. > http://github.com/cjfields/biome one of my to-do things for my holidays is to git clone it and star to play with it. I have several mOOse modules for GWAS that I am going to release soon but I would like to accomodate them first to the bioperl look and feel. > :) > > chris > > On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > >> >> extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: >> >> http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html >> >> I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. >> >> >> Have a good weekend >> >> -Pablo >> >> >> >> On Fri, 23 Jul 2010, Chris Fields wrote: >> >>> >>> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >>> >>>> On Fri, 23 Jul 2010, Dave Messina wrote: >>>> >>>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>>> >>>>> I did not know about local::lib. >>>>> >>>> >>>> [This is a bit off-topic but probably useful for core developers] >>>> Then probably you don't know about >>>> >>>> App::perlbrew >>>> >>>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >>> ... >>> >>> yes, just started using this myself. >>> >>> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >>> >>> chris >> >> >> ----- >> >> Pablo Marin-Garcia >> >> >> >> -- >> 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. > > ----- Pablo Marin-Garcia -- 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 sheetu.piscean at gmail.com Fri Jul 23 14:15:51 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 11:15:51 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> References: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> Message-ID: Thanks a lot Chris. It worked for me as well :) - Sheetal On Fri, Jul 23, 2010 at 10:36 AM, Chris Fields wrote: > I've attached the code and example data that worked. This is using the > latest bioperl on github, so maybe it's the version you have installed? > > chris > > On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > > I did remove that line but doesn't help. I still keep getting this > > error: > > MSG:

An error has occurred on > > the server, The server is unable to format right now, please try again > > in a few minutes. If the problem (Informational Message: No alias or > > index file found for protein database [nr/nt] in search path > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > 4KJE1YJ601N

> > > > Any pointers ?? > > > > - Sheetal > > > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > > wrote: > > Removing this line from your original script worked for me: > > > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > > > > This is set via '-prog' parameter. > > > > chris > > > > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > > > Yes the error is still occurring. I have emailed to > > Blast-help as well and they have to say that "there is > > something wrong with the URL, didn't give any specifics". > > > > > > Also changing the parameter SERVICE to 'plain' (by default > > it is set to plain, I guess this value is for standard blast > > pgm. like blastp, blastx, etc) gives me this error : > > > An error has occurred on the server, The server is unable to > > format right now, please try again in a few minutes. If the > > problem (Informational Message: No alias or index file found > > for protein database [nr/nt] in search path > > > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I > have sent an email today to blast-help for this error. > > > > > > Adding below the email conversation with blast-help for > > debugging further : > > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > > wrote: > > > Sheetal, > > > > > > You are right about the query syntax, but your URL has some > > errors. The URL below works; note that order of parameters > > does not matter. > > > > > > Best regards, > > > Wayne > > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > > 3EContig_236+%0A% > > > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > > > Thank you Wayne. I tried with the sequence beginning > > immediately after "QUERY=", (called as bare sequence) but > > still I get the same error. > > > > > > The documentation on your URLAPI says that Query can have > > Accession(s), gi(S) or FASTA sequence. The format of the query > > for FASTA sequence is as shown: > > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > > for FASTA sequence, the query has description/definition > > followed by actual sequence. In that case, the format of my > > POST request match the requirement. > > > > > > Can you help me figure out why am I still getting error : > > "Cannot accept request, error code: -103" ? Attaching the log > > file having Query as bare sequence and FASTA sequence for your > > reference. Your help is much appreciated. > > > > > > Thanks, > > > Sheetal > > > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > > wrote: > > > Hello, > > > > > > Our URLAPI, which your script should, but may or may not > > use, requires that the sequence begin immediately after > > "QUERY=". Your example shows a definition line preceding the > > sequence. You can get documentation on our URLAPI on this page > > (Web service interface): > > > > > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > > > Best regards, > > > Wayne > > > > > > _~___~___~__~__~_~ > > > Wayne Matten, PhD > > > NCBI Public Services > > > mattenw at mail.nih.gov > > > > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > Hello, > > > > > > I am trying to use blastx program with 'nr' database in my > > Bioperl script remotely. While I do so, I get this error : > > > Cannot accept request, error code: -103 > > > > > > The request that I send is : > > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > > bioperl-Bio_Tools_Run_ > > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > > 3EContig_236+% > > > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > > >> > > >> Can you please help me debug it. > > >> > > >> Thanks and Regards, > > >> Sheetal > > > > > > Thanks > > > Sheetal > > > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > > wrote: > > > The errors reported seem to indicate problems on the NCBI > > server, not problems with the script. Is this still > > occurring? > > > > > > chris > > > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > > Adding some more details on OS and BioPerl version > > > > > > > > OS: > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > > Jun 11 07:54:58 > > > > UTC 2010 i686 GNU/Linux > > > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > > > BioPerl Version : > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > > -MBio::Root::Version -e > > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > > 1.006001 > > > > > > > > Attached is the error that I get while running the > > RemoteBlast. > > > > > > > > Thanks, > > > > Sheetal > > > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > > wrote: > > > > > > > >> Hi, > > > >> > > > >> I am trying to run RemoteBlast to blastx sequences on > > 'nr' database. Here > > > >> is the complete script : > > > >> #Remote-blast "factory object" creation and > > blast-parameter > > > >> initialization > > > >> > > > >> use Bio::Tools::Run::RemoteBlast; > > > >> use strict; > > > >> my $prog = 'blastx'; > > > >> my $db = 'nr/nt'; > > > >> my $e_val= '1e-10'; > > > >> > > > >> my @params = ( '-prog' => $prog, > > > >> '-data' => $db, > > > >> '-expect' => $e_val, > > > >> '-readmethod' => 'SearchIO' ); > > > >> > > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > > >> > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; > > > >> > > > >> #$v is just to turn on and off the messages > > > >> my $v = 0; > > > >> > > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > > -format => 'fasta' > > > >> ); > > > >> > > > >> while (my $input = $str->next_seq()){ > > > >> #Blast a sequence against a database: > > > >> > > > >> #Alternatively, you could pass in a file with many > > > >> #sequences rather than loop through sequence one at a > > time > > > >> #Remove the loop starting 'while (my $input = > > $str->next_seq())' > > > >> #and swap the two lines below for an example of that. > > > >> my $r = $factory->submit_blast($input); > > > >> #my $r = $factory->submit_blast('amino.fa'); > > > >> > > > >> print STDERR "waiting..." if( $v > 0 ); > > > >> while ( my @rids = $factory->each_rid ) { > > > >> foreach my $rid ( @rids ) { > > > >> my $rc = $factory->retrieve_blast($rid); > > > >> if( !ref($rc) ) { > > > >> if( $rc < 0 ) { > > > >> print "removing rid as rc is < 0"; > > > >> $factory->remove_rid($rid); > > > >> } > > > >> print STDERR "." if ( $v > 0 ); > > > >> sleep 5; > > > >> } else { > > > >> my $result = $rc->next_result(); > > > >> #save the output > > > >> print "saving to file"; > > > >> my $filename = "contig_236.out"; # > > $result->query_name()."\.out"; > > > >> $factory->save_output($filename); > > > >> $factory->remove_rid($rid); > > > >> print "\nQuery Name: ", $result->query_name(), > > "\n"; > > > >> while ( my $hit = $result->next_hit ) { > > > >> next unless ( $v > 0); > > > >> print "\thit name is ", $hit->name, "\n"; > > > >> while( my $hsp = $hit->next_hsp ) { > > > >> print "\t\tscore is ", $hsp->score, "\n"; > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> > > > >> But when I run this, I get an error in html format which > > says "Cannot > > > >> accept request, error code: -103". Attaching the error > > file for reference. > > > >> Can you please help me with debugging this error? Your > > help is much > > > >> appreciated. > > > >> > > > >> Also, informing about the previous error that I fixed by > > adding this line: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; The error that > > > >> I was getting prior to adding this line was : > > > >> --------------------- WARNING --------------------- > > > >> MSG:

An error has > > occurred on the > > > >> server, The server is unable to format right now, please > > try again in a few > > > >> minutes. If the problem (Informational Message: No > > alias or index file > > > >> found for protein database [nr/nt] in search path > > > >> > > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > > RID: > > > >> 4CF5MY9101P

> > > >> > > > >> It kinda took me a while to find out the 2 > > requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > > >> > > > >> # 1) set your database like this: > > > >> -database => 'cdsearch/cdd', # c.f. > > > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > > >> > > > >> > > > >> # 2) add this line before submitting the job: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'rpsblast'; > > > >> > > > >> I think it will be great if you can add this to the > > synopsis section of > > > >> RemoteBlast.pm > > > >> > > > >> Thanks, > > > >> Sheetal > > > >> > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > From y-bushmanova at northwestern.edu Fri Jul 23 14:54:19 2010 From: y-bushmanova at northwestern.edu (Yulia Bushmanova) Date: Fri, 23 Jul 2010 13:54:19 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E26F.4020103@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> Message-ID: <4C49E55B.6000509@northwestern.edu> Sorry, first email had wrong file attached Yulia Yulia Bushmanova wrote: > Hi All, > > I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and > got following error: > > not well-formed (invalid token) at line 32, column 48, byte 3095 at > /usr/lib/perl5/XML/Parser.pm line 187 > > Looks like parser complains on the copyright sign, if I manually > remove it from file parsing goes fine. XML::Parser is version 2.36. > > Any ideas on how to deal with this error? > > Thanks in advance, > Yulia -------------- next part -------------- A non-text attachment was scrubbed... Name: allRefs_07232010.xml Type: text/xml Size: 42911 bytes Desc: not available URL: From David.Messina at sbc.su.se Fri Jul 23 15:00:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 13:00:07 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> Message-ID: <9C35A675-7A6C-4A33-8826-443CD4E5E541@sbc.su.se> Cool, thanks for the pointer to perlbrew! Dave From cjfields at illinois.edu Fri Jul 23 15:08:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 14:08:03 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E55B.6000509@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> <4C49E55B.6000509@northwestern.edu> Message-ID: <105D6D53-1465-44ED-BA6A-B2D642F09BA9@illinois.edu> You should file this as a bug, along with the output. My guess is it has to do with character encoding, but not sure. chris On Jul 23, 2010, at 1:54 PM, Yulia Bushmanova wrote: > Sorry, first email had wrong file attached > > Yulia > > Yulia Bushmanova wrote: >> Hi All, >> >> I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and got following error: >> >> not well-formed (invalid token) at line 32, column 48, byte 3095 at /usr/lib/perl5/XML/Parser.pm line 187 >> >> Looks like parser complains on the copyright sign, if I manually remove it from file parsing goes fine. XML::Parser is version 2.36. >> >> Any ideas on how to deal with this error? >> >> Thanks in advance, >> Yulia > > > > > > > 20643054 > > 2010 > 7 > 20 > >
> > 1542-0086 > > 99 > 2 > > 2010 > Jul > 21 > > > Biophysical journal > > Bimodal Analysis Reveals a General Scaling Law Governing Nondirected and Chemotactic Cell Motility. > > 367-376 > > > Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a nondirected fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses. Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multiscale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both nondirected and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines, indicating that the coupling of reorientation and persistence holds across species and making it possible to describe the complexity of cell motility in a surprisingly general and simple manner. With this new perspective, we analyzed the motility of Dictyostelium mutants, and found four in which the coupling between two modes was altered. Our results point to a fundamental underlying principle, described by a simple scaling law, unifying mechanisms of eukaryotic cell motility at several scales. > Copyright ? 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. > > Department of Pharmacology, Vanderbilt University, Nashville, Tennessee. > > > Gruver > J Scott > JS > > > Potdar > Alka A > AA > > > Jeon > Junhwan > J > > > Sai > Jiqing > J > > > Anderson > Bridget > B > > > Webb > Donna > D > > > Richmond > Ann > A > > > Quaranta > Vito > V > > > Cummings > Peter T > PT > > > Chung > Chang Y > CY > > > ENG > > JOURNAL ARTICLE > >
> > Biophys J > 0370626 > 0006-3495 > > > > > > 2009 > 12 > 17 > > > 2010 > 3 > 9 > > > 2010 > 3 > 11 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > ppublish > > S0006-3495(10)00710-1 > 10.1016/j.bpj.2010.03.073 > 20643054 > > > > > > > > 20640912 > > 2010 > 7 > 19 > >
> > 1420-9071 > > > 2010 > Jul > 18 > > > Cellular and molecular life sciences : CMLS > > Redundant and unique roles of coronin proteins in Dictyostelium. > > > > > Dictyostelium discoideum harbors a short (CRN12) and a long coronin (CRN7) composed of one and two beta-propellers, respectively. They are primarily present in the cell cortex and cells lacking CRN12 (corA (-)) or CRN7 (corB (-)) have defects in actin driven processes. We compared the characteristics of a mutant cell line (corA (-) /corB (-)) lacking CRN12 and CRN7 with the single mutants focusing on cytokinesis, phagocytosis, chemotaxis and development. Cytokinesis, uptake of small particles, and developmental defects were not enhanced in the corA (-) /corB (-) strain as compared to the single mutants, whereas motility and phagocytosis of yeast particles were more severely impaired. It appears that although both proteins affect the same processes they do not act in a redundant manner. Rather, they often act antagonistically, which is in accordance with their proposed roles in the actin cytoskeleton where CRN12 acts in actin disassembly whereas CRN7 stabilizes actin filaments and protects them from disassembly. > > Institute for Biochemistry I, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931, Cologne, Germany. > > > Shina > Maria C > MC > > > M?ller-Taubenberger > Annette > A > > > Unal > Can > C > > > Schleicher > Michael > M > > > Steinert > Michael > M > > > Eichinger > Ludwig > L > > > M?ller > Rolf > R > > > Blau-Wasser > Rosemarie > R > > > Gl?ckner > Gernot > G > > > Noegel > Angelika A > AA > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 18 > >
> > Cell Mol Life Sci > 9705402 > 1420-682X > > > > > > 2010 > 2 > 3 > > > 2010 > 7 > 5 > > > 2010 > 5 > 23 > > > 2010 > 7 > 18 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 10.1007/s00018-010-0455-y > 20640912 > > > > > > > > 20639697 > > 2010 > 7 > 19 > >
> > 1554-8635 > > 6 > 6 > > 2010 > Aug > 22 > > > Autophagy > > A second signal for autophagic cell death? > > > > > Dictyostelium cells in monolayers in vitro lend themselves well to a study of autophagic cell death (ACD). There is no apoptosis machinery in the protist Dictyostelium, no caspase nor Bcl-2 family members (except a paracaspase whose inactivation does not alter cell death), thus there is no apoptosis that could interfere with, or substitute for, nonapoptotic cell death. Also, Dictyostelium, a eukaryote, has a haploid genome, which facilitates random insertional mutagenesis. > > Centre d'Immunologie de Marseille-Luminy, Facult? des Sciences de Luminy, Aix Marseille Universit?, Marseille, France; Institut National de la Sant? et de la Recherche M?dicale U631, Marseille, France; Centre National de la Recherche Scientifique Unit? Mixte de Recherche, Marseille, France. > > > Giusti > Corinne > C > > > Luciani > Marie-Fran?oise > MF > > > Golstein > Pierre > P > > > ENG > > JOURNAL ARTICLE > > > 2010 > 8 > 22 > >
> > Autophagy > 101265188 > 1554-8627 > > > > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 12750 > 20639697 > > > > > > > > 20626455 > > 2010 > 7 > 19 > >
> > 1462-2920 > > > 2010 > Jul > 7 > > > Environmental microbiology > > The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa. > > > > > Summary The capacity of a bacterial pathogen to produce a disease in a treated host depends on the former's virulence and resistance to antibiotics. Several scattered pieces of evidence suggest that these two characteristics can be influenced by bacterial metabolism. This potential relationship is particularly important upon infection of a host, a situation that demands bacteria adapt their physiology to their new environment, making use of newly available nutrients. To explore the potential cross-talk between bacterial metabolism, antibiotic resistance and virulence, a Pseudomonas aeruginosa model was used. This species is an important opportunistic pathogen intrinsically resistant to many antibiotics. The role of Crc, a global regulator that controls the metabolism of carbon sources and catabolite repression in Pseudomonas, was analysed to determine its contribution to the intrinsic antibiotic resistance and virulence of P. aeruginosa. Using proteomic analyses, high-throughput metabolic tests and functional assays, the present work shows the virulence and antibiotic resistance of this pathogen to be linked to its physiology, and to be under the control (directly or indirectly) of Crc. A P. aeruginosa strain lacking the Crc regulator showed defects in type III secretion, motility, expression of quorum sensing-regulated virulence factors, and was less virulent in a Dictyostelium discoideum model. In addition, this mutant strain was more susceptible to beta-lactams, aminoglycosides, fosfomycin and rifampin. Crc might therefore be a good target in the search for new antibiotics. > > Departamento de Biotecnolog?a Microbiana, Centro Nacional de Biotecnolog?a, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain. > > > Linares > Juan F > JF > > > Moreno > Renata > R > > > Fajardo > Alicia > A > > > Mart?nez-Solano > Laura > L > > > Escalante > Ricardo > R > > > Rojo > Fernando > F > > > Mart?nez > Jos? L > JL > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 07 > >
> > Environ Microbiol > 100883692 > 1462-2912 > > > > > > 2010 > 7 > 15 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > aheadofprint > > EMI2292 > 10.1111/j.1462-2920.2010.02292.x > 20626455 > > > > > > > > 20624437 > > 2010 > 7 > 20 > >
> > 1873-5169 > > > 2010 > Jul > 16 > > > Peptides > > Synthesis and biological activity of peptides equivalent to the IP22 repeat motif found in proteins from Dictyostelium and Mimivirus. > > > > > A novel IP22 repeat motif of unknown function was discovered previously that comprises almost the entire structure of cmbB, a calmodulin-binding protein from Dictyostelium discoideum. An analysis of over 2000 IP22 repeats across 130 different proteins from different species allowed us to define a prototypical IP22 repeat: I/LPxxhxxhxhxxxhxxxhxxxx (where L=leucine, I=isoleucine, h=any hydrophobic amino acid, x=any amino acid). Here we describe the synthesis of three peptide variants of the IP22 motif: IP22-1 (IPNSVTSLKFGDGFNQPLTPGT; 22aa); IP22-2 (LPSTLKTISLSNSTDKKIFKNS; 22aa); and, IP22-3 (IPKSLRSLFLGKGYNQPLEF; 20aa) plus a control peptide from the N-term of cmbB (HNMNPFSPQLDEKKNSHIVEY; 21aa). The structure and purity of synthesized peptides were verified by HPLC and mass spectrometry. The peptides all dose-dependently enhanced random cell motility and cAMP-mediated chemotaxis in Dictyostelium but IP22-3 was most effective peaking in activity around 50muM. Fluorescein isothiocyanate (FITC)-conjugated IP22 peptides did not penetrate cells suggesting these peptides affect cell motility via cell surface interactions. Treatment of cells with FITC-IP22 peptides also led to enhanced cell motility equivalent to the non-conjugated peptides. Treatment of IP22-3-stimulated cells with 50muM LY294002, 20muM quinacrine or both suggests that IP22-3 requires both phosphoinositol 3-kinase and phospholipase A2 signaling to elicit its effects, a mechanism unique from EGFL motility enhancing peptides. The mechanism of action and potential uses of IP22 repeat peptides are discussed. > Copyright ? 2010. Published by Elsevier Inc. > > Department of Cell and Systems Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada, L5L 1C6; Department of Biology, University of Toronto at Mississauga, 3359 Mississauga rd. N., Mississauga, Ontario, Canada, L5L 1C6. > > > Catalano > Andrew > A > > > Luo > Wei > W > > > Wang > Yali > Y > > > O'Day > Danton H > DH > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 16 > >
> > Peptides > 8008690 > 0196-9781 > > > > > > 2010 > 6 > 22 > > > 2010 > 7 > 3 > > > 2010 > 7 > 5 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > aheadofprint > > S0196-9781(10)00300-1 > 10.1016/j.peptides.2010.07.005 > 20624437 > > > > > > > > 20617172 > > 2010 > 07 > 09 > >
> > 1553-7404 > > 6 > > 2010 > > > PLoS genetics > PLoS Genet. > > Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum. > > e1001013 > > > Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle. > > Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America. > > > Flowers > Jonathan M > JM > > > Li > Si I > SI > > > Stathos > Angela > A > > > Saxer > Gerda > G > > > Ostrowski > Elizabeth A > EA > > > Queller > David C > DC > > > Strassmann > Joan E > JE > > > Purugganan > Michael D > MD > > > eng > > Journal Article > Research Support, U.S. Gov't, Non-P.H.S. > > > 2010 > 07 > 01 > >
> > United States > PLoS Genet > 101239074 > 1553-7390 > > IM > PMC2895654 > > > > > 2010 > 3 > 15 > > > 2010 > 6 > 1 > > > 2010 > 7 > 1 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > epublish > > 10.1371/journal.pgen.1001013 > 20617172 > PMC2895654 > > > > > > > > 20610381 > > 2010 > 7 > 8 > >
> > 1083-351X > > > 2010 > Jul > 7 > > > The Journal of biological chemistry > > Expression of actin Tyr53Ala in Dictyostelium disrupts the cytoskeleton and inhibits intracellular and intercellular chemotactic-signaling. > > > > > We showed previously that phosphorylation of Tyr-53, or its mutation to Ala, inhibits actin polymerization in vitro with formation of aggregates of short filaments, and that expression of Y53A-actin in Dictyostelium blocks differentiation and development at the mound stage (Liu et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13694-13699; Liu et al. (2010) J. Biol. Chem. 285, 9729-9739). We now show that expression of Y53A-actin, which does not affect cell growth, phagocytosis or pinocytosis, inhibits the formation of head-to-tail cell streams during cAMP-induced aggregation, although individual amoebae chemotax normally. We show that expression of Y53A-actin causes a 50% reduction of cell-surface cAMP-receptors, and inhibits cAMP-induced increases in adenylyl cyclase A activity, phosphorylation of ERK2 and actin polymerization. Trafficking of vesicles containing adenylyl cyclase A to the rear of the cell and secretion of the ACA-vesicles are also inhibited. The actin cytoskeleton of cells expressing Y53A-actin is characterized by numerous short filaments, and bundled and aggregated filaments similar to the structures formed by copolymerization of purified Y53A-actin and wild-type actin in vitro. This disorganized actin cytoskeleton may be responsible for the inhibition of intracellular and intercellular cAMP signaling in cells expressing F-Y/A-actin. > > NHLBI, NIH, United States; > > > Shu > Shi > S > > > Liu > Xiong > X > > > Kriebel > Paul W > PW > > > Hong > Myoung-Soon > MS > > > Daniels > Mathew P > MP > > > Parent > Carole A > CA > > > Korn > Edward D > ED > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 7 > >
> > J Biol Chem > 2985121R > 0021-9258 > > > > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > aheadofprint > > M110.116277 > 10.1074/jbc.M110.116277 > 20610381 > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Fri Jul 23 19:04:38 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 23 Jul 2010 19:04:38 -0400 Subject: [Bioperl-l] reroot looses branch information Message-ID: Hi, I'm playing with some tree methods from Bio::Tree::TreeFunctionI and I found that Bio::Tree::TreeFunctionI::reroot looses the bootstrap support for the branch leading to the ancestor of the new root. Therefore, when calling reroot, I'm using code like my $ancestor = $newroot->ancestor; my $support = $newroot->bootstrap if (defined $ancestor); $tree->reroot($newroot); $ancestor->bootstrap($support) if (defined $support && defined $ancestor); There seems to be some code in reroot() to prevent that but I don't know why this is happening... Could you please check and fix that? Cheers, Robson From jason.stajich at gmail.com Sat Jul 24 12:41:30 2010 From: jason.stajich at gmail.com (Jason Stajich) Date: Sat, 24 Jul 2010 09:41:30 -0700 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <1125612054.776980.1279892924891.JavaMail.root@zimbra> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> Message-ID: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Hi. You should ask questions to the list. There are many who can answer your question there. In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. -Jason. Sent from my iPod On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > Hi Jason Stajich, > > I am using Bioperl and it is very useful. I have a question about > Bio::DB::GenBank. > This is a simple code. > > -------------------------- > > $db = Bio::DB::GenBank->new(); > @ids = ("LOC441435", "X78121"); > foreach $id (@ids){ > $seqobj = $db->get_Seq_by_id($id); > $seqstr = $seqobj->seq(); > print "$>id\n$seqstr\n"; > } > > -------------------------- > > If there is no entry for an ID, I would like to skip it and to get > next one. But this code stops running when an ID does not exist in > genbank. > How can I solve this problem? > > Thanks. > Hongseok Tae > From cjfields at illinois.edu Sat Jul 24 13:00:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 24 Jul 2010 12:00:24 -0500 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Message-ID: <9F83881D-6C9C-4996-95DF-D98C140DC3EB@illinois.edu> Any reason not to use a stream here? my $io = $db->get_Stream_by_id(\@ids); while (my $seq = $stream->next_seq) { # do stuff here } chris On Jul 24, 2010, at 11:41 AM, Jason Stajich wrote: > Hi. You should ask questions to the list. There are many who can answer your question there. > > In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. > > You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. > -Jason. > Sent from my iPod > > On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > >> Hi Jason Stajich, >> >> I am using Bioperl and it is very useful. I have a question about Bio::DB::GenBank. >> This is a simple code. >> >> -------------------------- >> >> $db = Bio::DB::GenBank->new(); >> @ids = ("LOC441435", "X78121"); >> foreach $id (@ids){ >> $seqobj = $db->get_Seq_by_id($id); >> $seqstr = $seqobj->seq(); >> print "$>id\n$seqstr\n"; >> } >> >> -------------------------- >> >> If there is no entry for an ID, I would like to skip it and to get next one. But this code stops running when an ID does not exist in genbank. >> How can I solve this problem? >> >> Thanks. >> Hongseok Tae >> > _______________________________________________ > 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 Jul 25 00:38:25 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jul 2010 00:38:25 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 Message-ID: Hi All, Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- MAJ From david.breimann at gmail.com Sun Jul 25 08:17:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 15:17:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") Message-ID: Hi, I'm using bp_genbank2gff3.pl and seems to work fine, but when I use the -y (split) option it always gives an error on the very last line of the genbank, whch is actually "//": For example, Can't use an undefined value as a symbol reference at /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. What's the problem? Thanks, Dave From dan.bolser at gmail.com Sun Jul 25 09:23:35 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 14:23:35 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? Message-ID: Hi all, The following bug report boils down to this question: How should two sequence objects be compared for identity? Does the object override 'eq' or implement an 'identical' method? I found the following apparent bug in Contig.pm while executing the documented 'SYNOPSIS' code: #!/usr/bin/perl -w use strict; use Bio::Assembly::Contig; my $c = Bio::Assembly::Contig-> new( -id => '1' ); my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' ); my $ls_coord = Bio::SeqFeature::Generic-> new( -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); $c->set_seq_coord( $ls_coord, $ls ); Gives the following WARNINGs: --------------------- WARNING --------------------- MSG: Adding sequence r1, which has already been added --------------------------------------------------- --------------------- WARNING --------------------- MSG: Replacing one sequence [r1] --------------------------------------------------- It seems to be a bug in the documented behaviour of set_seq_coord: "If the sequence was previously added using add_seq, its coordinates are changed/set. Otherwise, add_seq is called and the sequence is added to the contig." The offending line in that function seems to be: if( ... && ($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { ... } $self->add_seq($seq); which compares the *passed* sequence object to the sequence string for the *stored* sequence object of the same name. This comparison is always fails if I understood correctly, therefore set_seq_coord always spews warnings if called after add_seq. Out of curiosity, how come I can't just say: my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); I hope the above report can be of some use. Sincerely, Dan. From robfsouza at gmail.com Sun Jul 25 10:42:35 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sun, 25 Jul 2010 10:42:35 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Hi Dan, It is been a long time since I last loooked at this but, if I remember correctly, the point is that Bio:: On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: > The following bug report boils down to this question: > How should two sequence objects be compared for identity? Does the > object override 'eq' or implement an 'identical' method? I think an 'identical' or 'equal' method would be the best alternative since having a full method call would allow passing arguments like '-mode => "complete"' to check all sequence features and annotations if they exist and '-mode => "basic"' to check id() and seq() values. Bio::Assembly::Contig depends mostly on the last one, although only id() is tracked most of the time (because of the internal hashes). > I found the following apparent bug in Contig.pm while executing the > documented 'SYNOPSIS' code: [snip] > It seems to be a bug in the documented behaviour of set_seq_coord: > ? ? ? ?"If the sequence was previously added using add_seq, its > coordinates are changed/set. ?Otherwise, add_seq is called and the > sequence is added to the contig." In fact, it should not print warnings all the time.... > The offending line in that function seems to be: > ?if( ... && > ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { > ? ? ? ? ?... > ?} > ?$self->add_seq($seq); > which compares the *passed* sequence object to the sequence string for > the *stored* sequence object of the same name. This comparison is > always fails if I understood correctly, therefore set_seq_coord always > spews warnings if called after add_seq. Not the sequence string, but the objects themselves, i.e. the string perl uses to represent Bio::LocatableSeq objects... it is a memory based version of identical() :) > Out of curiosity, how come I can't just say: > my $ls = Bio::LocatableSeq-> > ?new( -seq ? ? ?=> 'ACCG-T', > ? ? ? -id ? ? ? => 'r1', > ? ? ? -alphabet => 'dna' > ? ? ? -start ? ?=> 3, > ? ? ? -end ? ? ?=> 8, > ? ? ? -strand ? => 1 > ? ? ); > $c->add_seq( $ls ); Oh, I don't remember but it was either a bad design decision I made 8 years ago to acommodate the Bio::Align::AlignI interface or a problem with Bio::SeqFeature::Collection at that time. Whatever the case, it would be nice to change it... you just need to create a Bio::SeqFeature::Generic when add_seq is called. I just won't have time to do it myself so feel free to act... Best, Robson > I hope the above report can be of some use. > > Sincerely, > Dan. > _______________________________________________ > 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 Sun Jul 25 12:35:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:35:42 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Cheers for the clarification Robson. How come the 'SYNOPSIS' code does produce warnings about replacing the seq? (the workaround is easy enough, don't add_seq, but still...) Since you said 'feel free to act', I have been faffing around here: http://github.com/dbolser/bioperl-live I'm not really sure if that is so useful, please advise. Thanks again for help, Dan. P.S. How come you are not in irc://irc.freenode.net/#bioperl ;-) On 25 July 2010 15:42, Robson de Souza wrote: > Hi Dan, > > It is been a long time since I last loooked at this but, if I remember > correctly, the point is that Bio:: > > On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >> The following bug report boils down to this question: >> How should two sequence objects be compared for identity? Does the >> object override 'eq' or implement an 'identical' method? > > I think an 'identical' or 'equal' method would be the best alternative > since having a full method call would allow passing arguments like > '-mode => "complete"' to check all sequence features and annotations > if they exist and '-mode => "basic"' to check id() and seq() values. > Bio::Assembly::Contig depends mostly on the last one, although only > id() is tracked most of the time (because of the internal hashes). > >> I found the following apparent bug in Contig.pm while executing the >> documented 'SYNOPSIS' code: > [snip] >> It seems to be a bug in the documented behaviour of set_seq_coord: >> ? ? ? ?"If the sequence was previously added using add_seq, its >> coordinates are changed/set. ?Otherwise, add_seq is called and the >> sequence is added to the contig." > > In fact, it should not print warnings all the time.... > >> The offending line in that function seems to be: >> ?if( ... && >> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >> ? ? ? ? ?... >> ?} >> ?$self->add_seq($seq); >> which compares the *passed* sequence object to the sequence string for >> the *stored* sequence object of the same name. This comparison is >> always fails if I understood correctly, therefore set_seq_coord always >> spews warnings if called after add_seq. > > Not the sequence string, but the objects themselves, i.e. the string > perl uses to represent Bio::LocatableSeq objects... it is a memory > based version of identical() :) > >> Out of curiosity, how come I can't just say: >> my $ls = Bio::LocatableSeq-> >> ?new( -seq ? ? ?=> 'ACCG-T', >> ? ? ? -id ? ? ? => 'r1', >> ? ? ? -alphabet => 'dna' >> ? ? ? -start ? ?=> 3, >> ? ? ? -end ? ? ?=> 8, >> ? ? ? -strand ? => 1 >> ? ? ); >> $c->add_seq( $ls ); > > Oh, I don't remember but it was either a bad design decision I made 8 > years ago to acommodate the Bio::Align::AlignI interface or a problem > with Bio::SeqFeature::Collection at that time. Whatever the case, it > would be nice to change it... you just need to create a > Bio::SeqFeature::Generic when > add_seq is called. I just won't have time to do it myself so feel free to act... > > Best, > Robson > >> I hope the above report can be of some use. >> >> Sincerely, >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From dan.bolser at gmail.com Sun Jul 25 12:40:21 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:40:21 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? Message-ID: Which objects implement SeqFeatureI, and how should I find that info? Sorry for the gratuitous noobs. Cheers, Dan. From genehack at genehack.org Sun Jul 25 14:06:55 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:06:55 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> (This is in reference to: ; sorry I'm not responding to the original message but I wasn't on the list at that point.) There are really two issues being reported here. First, bp_seqfeature_gff3.PLS throws the following error when used with Bio::SeqFeature::Store::DBI::SQLite: > Can't locate object method "gff3_string" via package "Bio::SeqFeature::Generic" at /Users/jhannah/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS line 58. Second, when called on a database that's been built with '$db->no_blobs(1)', the output doesn't actually include any features. I've got a fix for the first bug in . (I've submitted a pull request for that branch to the 'bioperl' user.) Basically, when looping over the feature objects in bp_seqfeature_gff3.PLS, we introspect each one to find out if it supports the gff3_string() or gff_string() methods, and either call the appropriate one or throw an exception. (I considered just calling gff_string() instead of doing the introspection, since (a) that's the interface documented in SeqFeatureI and (b) SeqFeature::Lite, which is the only thing that currently implements gff3_string() _also_ implements gff_string(), which recalls gff3_string() when appropriate, but in the end decided that this way preserves the original intent of the script as much as possible...) I'm working on something that may be a fix for the second issue as well, but thought I'd throw this first bit out for comments, being as this is the first change I've contributed back to the project. thanks, john. From genehack at genehack.org Sun Jul 25 14:36:07 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:36:07 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> Message-ID: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> On Jul 25, 2010, at 2:06 PM, John Anderson wrote: > Second, when called on a database that's been built with '$db->no_blobs(1)', the output [ snip ] I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. (A pull request for this change has been sent to the 'bioperl' user on Github.) thanks, john. From genehack at genehack.org Sun Jul 25 14:58:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:58:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > the -y (split) option it always gives an error on the very last line > of the genbank, whch is actually "//": > > For example, > > Can't use an undefined value as a symbol reference at > /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > > What's the problem? > I filed a bug for you; it's #3124 and can be seen at The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS > index 1216810..6bdae9d 100755 > --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > @@ -654,7 +654,7 @@ for my $file ( @files ) { > } > > ## FIXME for piped output w/ split FA files ... > - close($lumpfa_fh); > + close($lumpfa_fh) if $lumpfa_fh; > if (!$split && $outfa && $lump_fh) { > print $lump_fh "##FASTA\n"; # GFF3 spec > open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > > chrs, john. From cjfields at illinois.edu Sun Jul 25 15:18:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:18:41 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> Message-ID: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> On Jul 25, 2010, at 1:36 PM, John Anderson wrote: > On Jul 25, 2010, at 2:06 PM, John Anderson wrote: >> Second, when called on a database that's been built with '$db->no_blobs(1)', the output > [ snip ] > > I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. > > I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. > > (A pull request for this change has been sent to the 'bioperl' user on Github.) > > thanks, > john. On this one (in Bio::DB::SeqFeature::DBI::mysql): if ( $typeid and $db_seqid and $start and $end and $strand ) { # then we're good... } else { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Changing this to the following should work and is more direct: if ( !defined($typeid) || !defined($db_seqid) || !defined($start) || !defined($end) || !defined($strand) ) { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Might even work shortening to a grep: if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} chris From cjfields at illinois.edu Sun Jul 25 15:20:09 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:20:09 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Pull request was merged into master branch of bioperl-live. Thanks! Oddly, pull requests aren't coming through via the mail list, I'll look into the issue. chris On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use >> the -y (split) option it always gives an error on the very last line >> of the genbank, whch is actually "//": >> >> For example, >> >> Can't use an undefined value as a symbol reference at >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. >> >> What's the problem? >> > > I filed a bug for you; it's #3124 and can be seen at > > The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> index 1216810..6bdae9d 100755 >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> @@ -654,7 +654,7 @@ for my $file ( @files ) { >> } >> >> ## FIXME for piped output w/ split FA files ... >> - close($lumpfa_fh); >> + close($lumpfa_fh) if $lumpfa_fh; >> if (!$split && $outfa && $lump_fh) { >> print $lump_fh "##FASTA\n"; # GFF3 spec >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; >> >> > > chrs, > john. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Sun Jul 25 15:48:22 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 15:48:22 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: On Jul 25, 2010, at 3:18 PM, Chris Fields wrote: > On this one (in Bio::DB::SeqFeature::DBI::mysql): > > if ( $typeid and $db_seqid and $start and $end and $strand ) { Yeah, sorry, that sort of bugged me too, but once I got into testing stuff I forgot to go back and clean it up... > Might even work shortening to a grep: > > if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} Ended up with: # if we weren't called with all the params, pull those out of the database too if ( not ( grep { defined($_) } ( ... ))) { ... } because having the negation buried inside the grep block seemed confusing... I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) j. From david.breimann at gmail.com Sun Jul 25 15:52:53 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 22:52:53 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. Thanks! On Sun, Jul 25, 2010 at 10:20 PM, Chris Fields wrote: > Pull request was merged into master branch of bioperl-live. Thanks! > > Oddly, pull requests aren't coming through via the mail list, I'll look > into the issue. > > chris > > On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > > > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > > > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > >> the -y (split) option it always gives an error on the very last line > >> of the genbank, whch is actually "//": > >> > >> For example, > >> > >> Can't use an undefined value as a symbol reference at > >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > >> > >> What's the problem? > >> > > > > I filed a bug for you; it's #3124 and can be seen at < > http://bugzilla.open-bio.org/show_bug.cgi?id=3124> > > > > The following patch fixes it for me; it can be found in < > http://github.com/genehack/bioperl-live/tree/topic/bug-3124>. I've sent a > pull request for this change. > > > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS > b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> index 1216810..6bdae9d 100755 > >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> @@ -654,7 +654,7 @@ for my $file ( @files ) { > >> } > >> > >> ## FIXME for piped output w/ split FA files ... > >> - close($lumpfa_fh); > >> + close($lumpfa_fh) if $lumpfa_fh; > >> if (!$split && $outfa && $lump_fh) { > >> print $lump_fh "##FASTA\n"; # GFF3 spec > >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > >> > >> > > > > chrs, > > john. > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From genehack at genehack.org Sun Jul 25 16:05:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 16:05:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <139B16C1-C964-4C9A-AB7F-A6566749B215@genehack.org> On Jul 25, 2010, at 3:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Or you could just change the one line in the script yourself; that was the only change. > Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Could you send me (not the list, just me) an input file that produces this problem? > Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. It looks like the '-n' option should do that, but it currently throws a few more errors of the same general type as you were seeing before -- let me look at those... j. From David.Messina at sbc.su.se Sun Jul 25 16:34:42 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 25 Jul 2010 14:34:42 -0600 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> On Jul 25, 2010, at 13:48, John Anderson wrote: > > I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) You've probably seen this, right? http://www.bioperl.org/wiki/Bioperl_Best_Practices Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) Thanks for all your work on this, John! Dave From biopython at maubp.freeserve.co.uk Sun Jul 25 17:10:30 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 25 Jul 2010 22:10:30 +0100 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: On Sun, Jul 25, 2010 at 8:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view > to use to updated version should I first update my clone of bioperl-live > (git pull?) then go through the whole build and install again? > > Second, I have just noticed that bp_genbank2gff3.pl returns an error when > given a circular genome with a feature that spans the "end" of the genome > (e.g., assume the genome size is 1000np and a feature spans > join(900..1000,1..100). The GFF3 spec has recently been updated to cover circular genomes explicitly - this script probably needs updating in light of this. Peter From hlapp at drycafe.net Sun Jul 25 17:26:39 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 25 Jul 2010 17:26:39 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: Message-ID: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > Hi All, > Our BP poster from the conference is available on SlideShare (search > BioPerl ISMB 2010) and on my wiki homepage. Enjoy- If anyone was wondering about the URL: http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 Mark - were you going to post a news item on this? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sun Jul 25 19:05:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:05:49 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> Message-ID: <9F8B93B0-40B4-4D36-AFC8-42AB0F640E80@illinois.edu> On Jul 25, 2010, at 3:34 PM, Dave Messina wrote: > On Jul 25, 2010, at 13:48, John Anderson wrote: >> >> I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) > > You've probably seen this, right? > > http://www.bioperl.org/wiki/Bioperl_Best_Practices > > Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) > > Thanks for all your work on this, John! > > > > Dave Agreed, thanks John. I'll pull this into a local branch and test, then pull in if everything's okay. chris From cjfields at illinois.edu Sun Jul 25 19:09:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:22 -0500 Subject: [Bioperl-l] BOSC 2010 BioPerl slides Message-ID: <94B38B72-EC74-49AA-B8E6-7E0E0ABDEBFA@illinois.edu> Just a note that, along with Mark's poster, I gave a smallish update on BioPerl at BOSC 2010: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Feedback welcome! chris From cjfields at illinois.edu Sun Jul 25 19:09:35 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:35 -0500 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> Message-ID: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > > On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >> Hi All, >> Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > > If anyone was wondering about the URL: > > http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > > Mark - were you going to post a news item on this? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== We could do this along with posting the slides for the BOSC BioPerl talk: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl chris From cjfields at illinois.edu Sun Jul 25 19:11:06 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:11:06 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <9FB52BF8-532C-4FA2-A590-4ECDA9700E8B@illinois.edu> On Jul 25, 2010, at 4:10 PM, Peter wrote: > On Sun, Jul 25, 2010 at 8:52 PM, David Breimann > wrote: >> Thank you guys. I'm quite new to all this github stuff, so in order to view >> to use to updated version should I first update my clone of bioperl-live >> (git pull?) then go through the whole build and install again? >> >> Second, I have just noticed that bp_genbank2gff3.pl returns an error when >> given a circular genome with a feature that spans the "end" of the genome >> (e.g., assume the genome size is 1000np and a feature spans >> join(900..1000,1..100). > > The GFF3 spec has recently been updated to cover circular > genomes explicitly - this script probably needs updating in light > of this. > > Peter We need to add a few tests for circular genomes with BioPerl; I'm pretty sure these currently do not work as expected. chris From grapevine.256 at gmail.com Mon Jul 26 00:27:16 2010 From: grapevine.256 at gmail.com (Vidya Oruganti) Date: Mon, 26 Jul 2010 12:27:16 +0800 Subject: [Bioperl-l] Restriction Analysis Message-ID: Dear All, I am interested in knowing if there is a way to perform the restriction analysis module on many sequences at once. Currently I am retrieving sequences of contigs one by one from genbank and performing the restriction analysis individually. This is the script I am using: use Bio::Restriction::Analysis; use Bio::DB::GenBank; use Data::Dumper; use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); $seq = $gb->get_Seq_by_gi('405830'); # GI Number my $ra = Bio::Restriction::Analysis->new(-seq=>$seq); print "There are ", scalar $ra->zero_cutters->each_enzyme, " enzymes that do not cut\n"; printf "\n%-10s%s\n", 'Enzyme', 'Number of Cuts'; my $all_cutters = $ra->cutters; map { printf "%-10s%s\n", $_->name, $ra->cuts_by_enzyme($_->name) } $all_cutters->each_enzyme; I would like to know whether it would be possible to get an array of sequences from genbank instead of just one and run the restriction analysis on all the sequences at one go and get several outputs at once. I have been able to retrieve more than one sequence from genbank but I'm not able to run the analysis on more than one sequence. Thank you From adsj at novozymes.com Mon Jul 26 03:09:54 2010 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 26 Jul 2010 09:09:54 +0200 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> (Chris Fields's message of "Sun, 25 Jul 2010 18:09:35 -0500") References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> Message-ID: <87eieqen25.fsf@topper.koldfront.dk> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> Our BP poster from the conference is available on SlideShare (search >>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Any chance of posting these slides for download somewhere that doesn't require creating an account to do so? Best wishes, Adam, just curious. -- Adam Sj?gren adsj at novozymes.com From avilella at gmail.com Mon Jul 26 05:08:32 2010 From: avilella at gmail.com (Albert Vilella) Date: Mon, 26 Jul 2010 10:08:32 +0100 Subject: [Bioperl-l] Run wrappers for BWA and Samtools In-Reply-To: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> References: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> Message-ID: Hi Mark, First of all, great work. Can I ask if the aim of combining bwa and samtools would be or could be to replicate "maq.pl easyrun" ? Or what would be an alternative for users wanting to do "maq.pl easyrun" for a combination of long and short reads? Cheers, Albert. On Sat, Nov 28, 2009 at 5:23 PM, Mark A. Jensen wrote: > Hi All, > > Run wrappers for the bwa assembler and the samtools suite > are now available as beta in the bioperl-run/trunk. The bwa > wrapper allows you to run a canned assembly pipeline, or > to execute individual bwa components. The assembly pipeline > can return a Bio::Assembly::Scaffold object via the new > Bio::Assembly::IO::sam module in bioperl-live/trunk > (this requires lstein's Bio::DB::Sam, from CPAN). Details at > > http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA > > and, of course, in the pod. > > Cheers, > MAJ > _______________________________________________ > 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 Jul 26 09:38:01 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:38:01 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 Message-ID: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.com > > _______________________________________________ > 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 Jul 26 09:18:56 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:18:56 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Hi Benard, Forwarding to the list for more help for you. You may want to look at the POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to use this module to create an OrthoMCL wrapper. This might be more technical than you want. Maybe a dev on the list would be interested in creating a wrapper using CommandExts. cheers, MAJ ----- Original Message ----- From: "Benard Kulohoma" To: Sent: Wednesday, July 21, 2010 10:58 AM Subject: Inquiry Hi Mark, I just read your bioperl resource on BWA (and here: http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was most helpful. Do you have any idea of how I could use Bioperl to implement OrthoMCL of several bacterial genomes. I would like to find some membrane proteins. Many thanks, Benard PS: I am sorry for spaming/inquiring!! :) -- 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 roy.chaudhuri at gmail.com Mon Jul 26 09:46:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 26 Jul 2010 14:46:49 +0100 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: <4C4D91C9.4090704@gmail.com> Thanks for this Mark. Just in case anyone can't find it, it's here: http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png Roy. On 26/07/2010 14:38, Mark A. Jensen wrote: > missed the list-- > ----- Original Message ----- > From: "Mark A. Jensen" > To: "Adam "Sj?gren"" > Sent: Monday, July 26, 2010 9:37 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > >> There's a png version of the poster on my wiki page >> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >> wiki thinks it should?). Chris, maybe could upload yours to wiki? >> cheers MAJ >> ----- Original Message ----- >> From: "Adam "Sj?gren"" >> To: >> Sent: Monday, July 26, 2010 3:09 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >> >>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> >>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >> >>>>> Our BP poster from the conference is available on SlideShare (search >>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> >>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >> >>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >> >> Any chance of posting these slides for download somewhere that doesn't >> require creating an account to do so? >> >> >> Best wishes, >> >> Adam, just curious. >> >> -- >> Adam Sj?gren >> adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 09:46:38 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:46:38 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: http://bioperl.org/wiki/Mark_Jensen, it is... ----- Original Message ----- From: "Mark A. Jensen" To: "BioPerl List" Sent: Monday, July 26, 2010 9:38 AM Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 10:05:12 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 10:05:12 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4C4D91C9.4090704@gmail.com> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: http://posters.f1000.com/PosterList?posterID=246 ----- Original Message ----- From: "Roy Chaudhuri" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, July 26, 2010 9:46 AM Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > Thanks for this Mark. Just in case anyone can't find it, it's here: > http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png > > Roy. > > On 26/07/2010 14:38, Mark A. Jensen wrote: >> missed the list-- >> ----- Original Message ----- >> From: "Mark A. Jensen" >> To: "Adam "Sj?gren"" >> Sent: Monday, July 26, 2010 9:37 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >>> There's a png version of the poster on my wiki page >>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with >>> uploading >>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>> cheers MAJ >>> ----- Original Message ----- >>> From: "Adam "Sj?gren"" >>> To: >>> Sent: Monday, July 26, 2010 3:09 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>> >>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>> >>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> >>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>> >>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>> >>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>> >>> Any chance of posting these slides for download somewhere that doesn't >>> require creating an account to do so? >>> >>> >>> Best wishes, >>> >>> Adam, just curious. >>> >>> -- >>> Adam Sj?gren >>> adsj at novozymes.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 amackey at virginia.edu Mon Jul 26 10:51:43 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Mon, 26 Jul 2010 10:51:43 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes sense to "wrap" it. See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt -Aaron On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > Hi Benard, > Forwarding to the list for more help for you. You may want to look at the > POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live > distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to > use this module to create an OrthoMCL wrapper. This might be more technical > than you want. Maybe a dev on the list would be interested in creating a > wrapper using CommandExts. > cheers, MAJ > ----- Original Message ----- From: "Benard Kulohoma" < > B.Kulohoma at liverpool.ac.uk> > To: > Sent: Wednesday, July 21, 2010 10:58 AM > Subject: Inquiry > > > Hi Mark, > > I just read your bioperl resource on BWA (and here: > http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was > most helpful. Do you have any idea of how I could use Bioperl to implement > OrthoMCL of several bacterial genomes. I would like to find some membrane > proteins. > > Many thanks, > > Benard > > PS: I am sorry for spaming/inquiring!! :) > > -- > 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. > > > _______________________________________________ > 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 Jul 26 11:05:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 10:05:05 -0500 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: <84B78CA5-5D0E-447C-B507-8FCA18EDA7CB@illinois.edu> Agreed; I'm using it locally. I could see subclassing BLAST (or similar) wrappers specifically for the all-v-all portion of the pipeline (for consistency/flexibility), but I get along w/o that. chris On Jul 26, 2010, at 9:51 AM, Aaron Mackey wrote: > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 maj at fortinbras.us Mon Jul 26 11:07:35 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 11:07:35 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Maybe not in the sense of CommandExts, but a BioPerl module that does the "13 steps" might be very useful. (Not saying anyone should do it :) ) ----- Original Message ----- From: "Aaron Mackey" To: "Mark A. Jensen" Cc: "BioPerl List" ; "Benard Kulohoma" Sent: Monday, July 26, 2010 10:51 AM Subject: Re: [Bioperl-l] Inquiry on OrthoMCL > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Jul 26 11:35:18 2010 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jul 2010 11:35:18 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, I think there are probably several BioPerl classes that implement Bio::SeqFeatureI, like Bio::SeqFeature::Generic. What are you looking for? Scott On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: > Which objects implement SeqFeatureI, and how should I find that info? > > Sorry for the gratuitous noobs. > > Cheers, > Dan. > _______________________________________________ > 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 Mon Jul 26 12:22:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 11:22:54 -0500 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: I've added the PDF version of the BOSC 2010 talk and both the PDF and .ppt versions of the ISMB 2010 BioPerl poster here: http://www.bioperl.org/DIST/presentations/ Just a warning, the PDF of the poster has copyright notices all over it (I'll post a clean one if it's emailed to me!). Mark, did you want to make a blog post about these? chris On Jul 26, 2010, at 9:05 AM, Mark A. Jensen wrote: > Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: > http://posters.f1000.com/PosterList?posterID=246 > ----- Original Message ----- From: "Roy Chaudhuri" > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Monday, July 26, 2010 9:46 AM > Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > > >> Thanks for this Mark. Just in case anyone can't find it, it's here: >> http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png >> >> Roy. >> >> On 26/07/2010 14:38, Mark A. Jensen wrote: >>> missed the list-- >>> ----- Original Message ----- >>> From: "Mark A. Jensen" >>> To: "Adam "Sj?gren"" >>> Sent: Monday, July 26, 2010 9:37 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>>> There's a png version of the poster on my wiki page >>>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >>>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>>> cheers MAJ >>>> ----- Original Message ----- >>>> From: "Adam "Sj?gren"" >>>> To: >>>> Sent: Monday, July 26, 2010 3:09 AM >>>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>>> >>>> >>>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>>> >>>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>>> >>>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>>> >>>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>>> >>>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>>> >>>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>>> >>>> Any chance of posting these slides for download somewhere that doesn't >>>> require creating an account to do so? >>>> >>>> >>>> Best wishes, >>>> >>>> Adam, just curious. >>>> >>>> -- >>>> Adam Sj?gren >>>> adsj at novozymes.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 >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Mon Jul 26 13:54:22 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Mon, 26 Jul 2010 13:54:22 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: > Thanks again Robson, > > One thing I was going to email the list about is a lack of tests for > ace.pm and phrap.pm ... because of missing libs I'm not running the > sam or the maq tests, so any changes that I'm making to Contig.pm / > Scaffold.pm are not really being tested. > > Do you think anyone on the list (or you) would be able to generate a > few hundred tests to help me start modifying code with confidence? I hope so. I was reading Chris's presentation at BOSC and he mentioned that people are working on the support for the samtools so I believe somebody must have a dataset they could share. > One idea was to actually make Contig.pm implement SeqFeatureI, so that > you could call start and end and seq on the contig (consensus) > directly. > > Here are some notes from IRC... > > 04:00 < dbolser> I think "$contig_object->start" is totally reasonable > 04:01 < dbolser> otherwise its something like > "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" > 04:02 < dbolser> (untested ;-) > 09:01 < genehack> dbolser: i think you've got an argument that there should be; > it's probably going to be a lot easier to do that in > something like Biome (i.e., BioPerl in Moose) Never thought about it... but I can see that could be useful when contigs are part of higher level assemblies, like scaffolds or assembled chromosomes, but you could also achieve this by making Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any reason to prefer the Bio::SeqFeatureI interface? > Any reason not to cc this to the list? Lack of attention. I was so concerned about the answer that I didn't notice I pressed "Reply to" :) Best, Robson > Thanks again. > > All the best, > Dan. > > > > > On 26 July 2010 17:23, Robson de Souza wrote: >> Hi, >> >> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>> Cheers for the clarification Robson. >> >> You are welcome :). Thanks for improving my long abandoned child... :) >> >>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>> seq? (the workaround is easy enough, don't add_seq, but still...) >> >> I don't know. I remember testing it while I develop Contig.pm in >> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >> Did you try ace.pm recently? It uses set_seq_coord and this method >> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >> of previous bug reports on ace.pm regarding unexpected warnings... >> note that set_seq_coord calls remove_seq before adding but prints >> another warning. Compare set_seq_coord to add_seq alone and maybe you >> will figure out what is going on... >> >> Regarding why you can't just add Bio::LocatableSeq objects and have >> add_seq just set the coordinates by itself, I investigated my long >> forgotten code and just realized that the whole problem was that the >> coordinates of a Bio::LocatableSeq object represent the location of >> the object in the original sequence (i.e. unaligned read coordinates) >> instead of its coordinates in the aligned consensus sequence. >> Bio::LocatableSeq issues a warning whenever you try to set the object >> start and end coordinates to the gapped consensus coordinates because >> such coordinates lead to a length shorter than the actual read length: >> >> use Bio::LocatableSeq; >> use Bio::SeqFeature::Collection; >> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >> =>"agggcACT-Gccc", -id=>"uga"); >> my $sfc = Bio::SeqFeature::Collection->new(); >> $sfc->add_features([ $ls ]); >> print $sfc->feature_count,"\t",$ls->length."\n"; >> >> Additionally, Bio::LocatableSeq objects do not support the >> primary_tag() method because they are just Bio::RangeI and not >> Bio::SeqFeatureI objects. These two issues prevented me from using >> Bio::LocatableSeq coordinates to represent gapped consensus >> coordinates but the example code above suggests suppressing >> Bio::LocatableSeq warnings and using the object class >> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >> the need for extra Bio::SeqFeature::Generic objects to store read >> coordinates. >> >>> Since you said 'feel free to act', I have been faffing around here: >>> http://github.com/dbolser/bioperl-live >>> I'm not really sure if that is so useful, please advise. >> >> The comments I made above points to one area where you could have some >> improvements in both memory usage and usability: drop the need for >> additional Bio::SeqFeatureI objects to represent gapped consensus >> coordinates. It would require you to check all Contig.pm methods for >> the use of the "_aligned_coord:$readID" tags (I don't expect to see >> any references to this outside Contig.pm) and change set_seq_coord to >> a method that changes/sets the start and end values of the >> Bio::LocatableSeq objects. >> This might be a bit of work so just go for it if you want and have >> time to experiment. >> >> Another detail: could you please replace references in Contig.pm and >> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >> not exists to the correct Bio::* classes? Somebody changed this to the >> wrong names long ago... >> >>> Thanks again for help, >> >> Well these are my thoughts on the matter. Write again if you decide to >> take this on and are unable to make progress. >> Best, >> Robson >> >>> Dan. >>> >>> >>> P.S. >>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>> >>> >>> On 25 July 2010 15:42, Robson de Souza wrote: >>>> Hi Dan, >>>> >>>> It is been a long time since I last loooked at this but, if I remember >>>> correctly, the point is that Bio:: >>>> >>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>> The following bug report boils down to this question: >>>>> How should two sequence objects be compared for identity? Does the >>>>> object override 'eq' or implement an 'identical' method? >>>> >>>> I think an 'identical' or 'equal' method would be the best alternative >>>> since having a full method call would allow passing arguments like >>>> '-mode => "complete"' to check all sequence features and annotations >>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>> id() is tracked most of the time (because of the internal hashes). >>>> >>>>> I found the following apparent bug in Contig.pm while executing the >>>>> documented 'SYNOPSIS' code: >>>> [snip] >>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>> sequence is added to the contig." >>>> >>>> In fact, it should not print warnings all the time.... >>>> >>>>> The offending line in that function seems to be: >>>>> ?if( ... && >>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>> ? ? ? ? ?... >>>>> ?} >>>>> ?$self->add_seq($seq); >>>>> which compares the *passed* sequence object to the sequence string for >>>>> the *stored* sequence object of the same name. This comparison is >>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>> spews warnings if called after add_seq. >>>> >>>> Not the sequence string, but the objects themselves, i.e. the string >>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>> based version of identical() :) >>>> >>>>> Out of curiosity, how come I can't just say: >>>>> my $ls = Bio::LocatableSeq-> >>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>> ? ? ? -id ? ? ? => 'r1', >>>>> ? ? ? -alphabet => 'dna' >>>>> ? ? ? -start ? ?=> 3, >>>>> ? ? ? -end ? ? ?=> 8, >>>>> ? ? ? -strand ? => 1 >>>>> ? ? ); >>>>> $c->add_seq( $ls ); >>>> >>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>> would be nice to change it... you just need to create a >>>> Bio::SeqFeature::Generic when >>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>> >>>> Best, >>>> Robson >>>> >>>>> I hope the above report can be of some use. >>>>> >>>>> Sincerely, >>>>> Dan. >>>>> _______________________________________________ >>>>> 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 Tue Jul 27 04:53:49 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 09:53:49 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 26 July 2010 16:35, Scott Cain wrote: > Hi Dan, > > I think there are probably several BioPerl classes that implement > Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking > for? A way to find what implements what... something like javadoc for bp. Really I'm looking for a nice 'ontology' of SeqFeatures. I was thinking that Contig.pm should implement Bio::SeqFeatureI. > Scott > > > On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >> Which objects implement SeqFeatureI, and how should I find that info? >> >> Sorry for the gratuitous noobs. >> >> Cheers, >> Dan. >> _______________________________________________ >> 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 dan.bolser at gmail.com Tue Jul 27 05:02:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 10:02:05 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On 26 July 2010 18:54, Robson de Souza wrote: > On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >> Thanks again Robson, >> >> One thing I was going to email the list about is a lack of tests for >> ace.pm and phrap.pm ... because of missing libs I'm not running the >> sam or the maq tests, so any changes that I'm making to Contig.pm / >> Scaffold.pm are not really being tested. >> >> Do you think anyone on the list (or you) would be able to generate a >> few hundred tests to help me start modifying code with confidence? > > I hope so. I was reading Chris's presentation at BOSC and he mentioned > that people are working on the support for the samtools so I believe > somebody must have a dataset they could share. Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because I don't have samtools installed. Also, (quick impression) method coverage is limited (Contig.pm has a lot of methods!). I'll try to write some tests for ace.pm and phrap.pm. >> One idea was to actually make Contig.pm implement SeqFeatureI, so that >> you could call start and end and seq on the contig (consensus) >> directly. >> >> Here are some notes from IRC... >> >> 04:00 < dbolser> I think "$contig_object->start" is totally reasonable >> 04:01 < dbolser> otherwise its something like >> "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" >> 04:02 < dbolser> (untested ;-) >> 09:01 < genehack> dbolser: i think you've got an argument that there should be; >> ? ? ? ? ? ? ? ? ?it's probably going to be a lot easier to do that in >> ? ? ? ? ? ? ? ? ?something like Biome (i.e., BioPerl in Moose) > > Never thought about it... but I can see that could be useful when > contigs are part of higher level assemblies, like scaffolds or > assembled chromosomes, but you could also achieve this by making > Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any > reason to prefer the Bio::SeqFeatureI interface? No. I don't have an overview of how the various objects relate to one another, so any choice is more or less arbitrary. I'll try to write a 'Sequence HOWTO'. Thanks again for help, Dan. >> Any reason not to cc this to the list? > > Lack of attention. I was so concerned about the answer that I didn't > notice I pressed "Reply to" :) > Best, > Robson > >> Thanks again. >> >> All the best, >> Dan. >> >> >> >> >> On 26 July 2010 17:23, Robson de Souza wrote: >>> Hi, >>> >>> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>>> Cheers for the clarification Robson. >>> >>> You are welcome :). Thanks for improving my long abandoned child... :) >>> >>>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>>> seq? (the workaround is easy enough, don't add_seq, but still...) >>> >>> I don't know. I remember testing it while I develop Contig.pm in >>> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >>> Did you try ace.pm recently? It uses set_seq_coord and this method >>> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >>> of previous bug reports on ace.pm regarding unexpected warnings... >>> note that set_seq_coord calls remove_seq before adding but prints >>> another warning. Compare set_seq_coord to add_seq alone and maybe you >>> will figure out what is going on... >>> >>> Regarding why you can't just add Bio::LocatableSeq objects and have >>> add_seq just set the coordinates by itself, I investigated my long >>> forgotten code and just realized that the whole problem was that the >>> coordinates of a Bio::LocatableSeq object represent the location of >>> the object in the original sequence (i.e. unaligned read coordinates) >>> instead of its coordinates in the aligned consensus sequence. >>> Bio::LocatableSeq issues a warning whenever you try to set the object >>> start and end coordinates to the gapped consensus coordinates because >>> such coordinates lead to a length shorter than the actual read length: >>> >>> use Bio::LocatableSeq; >>> use Bio::SeqFeature::Collection; >>> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >>> =>"agggcACT-Gccc", -id=>"uga"); >>> my $sfc = Bio::SeqFeature::Collection->new(); >>> $sfc->add_features([ $ls ]); >>> print $sfc->feature_count,"\t",$ls->length."\n"; >>> >>> Additionally, Bio::LocatableSeq objects do not support the >>> primary_tag() method because they are just Bio::RangeI and not >>> Bio::SeqFeatureI objects. These two issues prevented me from using >>> Bio::LocatableSeq coordinates to represent gapped consensus >>> coordinates but the example code above suggests suppressing >>> Bio::LocatableSeq warnings and using the object class >>> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >>> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >>> the need for extra Bio::SeqFeature::Generic objects to store read >>> coordinates. >>> >>>> Since you said 'feel free to act', I have been faffing around here: >>>> http://github.com/dbolser/bioperl-live >>>> I'm not really sure if that is so useful, please advise. >>> >>> The comments I made above points to one area where you could have some >>> improvements in both memory usage and usability: drop the need for >>> additional Bio::SeqFeatureI objects to represent gapped consensus >>> coordinates. It would require you to check all Contig.pm methods for >>> the use of the "_aligned_coord:$readID" tags (I don't expect to see >>> any references to this outside Contig.pm) and change set_seq_coord to >>> a method that changes/sets the start and end values of the >>> Bio::LocatableSeq objects. >>> This might be a bit of work so just go for it if you want and have >>> time to experiment. >>> >>> Another detail: could you please replace references in Contig.pm and >>> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >>> not exists to the correct Bio::* classes? Somebody changed this to the >>> wrong names long ago... >>> >>>> Thanks again for help, >>> >>> Well these are my thoughts on the matter. Write again if you decide to >>> take this on and are unable to make progress. >>> Best, >>> Robson >>> >>>> Dan. >>>> >>>> >>>> P.S. >>>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>>> >>>> >>>> On 25 July 2010 15:42, Robson de Souza wrote: >>>>> Hi Dan, >>>>> >>>>> It is been a long time since I last loooked at this but, if I remember >>>>> correctly, the point is that Bio:: >>>>> >>>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>>> The following bug report boils down to this question: >>>>>> How should two sequence objects be compared for identity? Does the >>>>>> object override 'eq' or implement an 'identical' method? >>>>> >>>>> I think an 'identical' or 'equal' method would be the best alternative >>>>> since having a full method call would allow passing arguments like >>>>> '-mode => "complete"' to check all sequence features and annotations >>>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>>> id() is tracked most of the time (because of the internal hashes). >>>>> >>>>>> I found the following apparent bug in Contig.pm while executing the >>>>>> documented 'SYNOPSIS' code: >>>>> [snip] >>>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>>> sequence is added to the contig." >>>>> >>>>> In fact, it should not print warnings all the time.... >>>>> >>>>>> The offending line in that function seems to be: >>>>>> ?if( ... && >>>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>>> ? ? ? ? ?... >>>>>> ?} >>>>>> ?$self->add_seq($seq); >>>>>> which compares the *passed* sequence object to the sequence string for >>>>>> the *stored* sequence object of the same name. This comparison is >>>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>>> spews warnings if called after add_seq. >>>>> >>>>> Not the sequence string, but the objects themselves, i.e. the string >>>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>>> based version of identical() :) >>>>> >>>>>> Out of curiosity, how come I can't just say: >>>>>> my $ls = Bio::LocatableSeq-> >>>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>>> ? ? ? -id ? ? ? => 'r1', >>>>>> ? ? ? -alphabet => 'dna' >>>>>> ? ? ? -start ? ?=> 3, >>>>>> ? ? ? -end ? ? ?=> 8, >>>>>> ? ? ? -strand ? => 1 >>>>>> ? ? ); >>>>>> $c->add_seq( $ls ); >>>>> >>>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>>> would be nice to change it... you just need to create a >>>>> Bio::SeqFeature::Generic when >>>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>>> >>>>> Best, >>>>> Robson >>>>> >>>>>> I hope the above report can be of some use. >>>>>> >>>>>> Sincerely, >>>>>> Dan. >>>>>> _______________________________________________ >>>>>> 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 Jul 27 09:45:25 2010 From: scott at scottcain.net (Scott Cain) Date: Tue, 27 Jul 2010 09:45:25 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, You might find the deobfuscator helpful: http://bioperl.org/cgi-bin/deob_interface.cgi Scott On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: > On 26 July 2010 16:35, Scott Cain wrote: >> Hi Dan, >> >> I think there are probably several BioPerl classes that implement >> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >> for? > > A way to find what implements what... something like javadoc for bp. > > Really I'm looking for a nice 'ontology' of SeqFeatures. > > I was thinking that Contig.pm should implement Bio::SeqFeatureI. > > >> Scott >> >> >> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>> Which objects implement SeqFeatureI, and how should I find that info? >>> >>> Sorry for the gratuitous noobs. >>> >>> Cheers, >>> Dan. >>> _______________________________________________ >>> 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 >> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 Ontario Institute for Cancer Research From twaddlac at gmail.com Tue Jul 27 10:10:30 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:10:30 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: Hello, I am curious as to how I am supposed to use SeqIO::fastq to read in a fastq file and then obtain the nucleotide sequence from that. I noticed that SeqIO::fastq returns a Seq::Quality object but I haven't seen a method within that module that returns the nucleotide sequence. Please, let me know if you have any suggestions! Thank you very much!! -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 10:16:27 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:16:27 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: Message-ID: <4C4EEA3B.6020803@gmail.com> Hi Alan, Another case for the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say $seqqual->seq to get the sequence as a string. Cheers. Roy. On 27/07/2010 15:10, Alan Twaddle wrote: > Hello, > > I am curious as to how I am supposed to use SeqIO::fastq to read > in a fastq file and then obtain the nucleotide sequence from that. I > noticed that SeqIO::fastq returns a Seq::Quality object but I haven't > seen a method within that module that returns the nucleotide sequence. > Please, let me know if you have any suggestions! > > Thank you very much!! > From cjfields at illinois.edu Tue Jul 27 10:34:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 09:34:54 -0500 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Jul 27, 2010, at 4:02 AM, Dan Bolser wrote: > On 26 July 2010 18:54, Robson de Souza wrote: >> On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >>> Thanks again Robson, >>> >>> One thing I was going to email the list about is a lack of tests for >>> ace.pm and phrap.pm ... because of missing libs I'm not running the >>> sam or the maq tests, so any changes that I'm making to Contig.pm / >>> Scaffold.pm are not really being tested. >>> >>> Do you think anyone on the list (or you) would be able to generate a >>> few hundred tests to help me start modifying code with confidence? >> >> I hope so. I was reading Chris's presentation at BOSC and he mentioned >> that people are working on the support for the samtools so I believe >> somebody must have a dataset they could share. > > Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because > I don't have samtools installed. Also, (quick impression) method > coverage is limited (Contig.pm has a lot of methods!). > > I'll try to write some tests for ace.pm and phrap.pm. Tests are good! >> Never thought about it... but I can see that could be useful when >> contigs are part of higher level assemblies, like scaffolds or >> assembled chromosomes, but you could also achieve this by making >> Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any >> reason to prefer the Bio::SeqFeatureI interface? > > No. I don't have an overview of how the various objects relate to one > another, so any choice is more or less arbitrary. I'll try to write a > 'Sequence HOWTO'. > > > Thanks again for help, > Dan. Dan, The current HOWTOs (Beginner's, Feature/Annotation) should have this information, along with the BioPerl tutorial. chris From twaddlac at gmail.com Tue Jul 27 10:38:09 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:38:09 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EEA3B.6020803@gmail.com> References: <4C4EEA3B.6020803@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: > Hi Alan, > > Another case for the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi > > A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say > $seqqual->seq to get the sequence as a string. > > Cheers. > Roy. > > On 27/07/2010 15:10, Alan Twaddle wrote: >> >> Hello, >> >> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >> in a fastq file and then obtain the nucleotide sequence from that. I >> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >> seen a method within that module that returns the nucleotide sequence. >> Please, let me know if you have any suggestions! >> >> Thank you very much!! >> > > -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 10:50:21 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:50:21 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> Message-ID: <4C4EF22D.6050705@gmail.com> Hi Alan, It sounds like there's a problem with reading in your Fastq file. Are you using the latest BioPerl version? There have been many bug fixes to Bio::SeqIO::fastq over the last couple of years. If you are using an up-to-date BioPerl, please could you send an example Fastq entry which gives the error messages? Roy. On 27/07/2010 15:37, Alan Twaddle wrote: > Whenever I try to access the sequence I get the following error message: > > > --------------------- WARNING --------------------- > MSG: Seq/Qual descriptions don't match; using sequence description > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Fastq sequence/quality data length mismatch error > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + > --------------------------------------------------- > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Attempting to set the sequence to > [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] > which does not look healthy > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 > STACK: Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 > STACK: Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 > STACK: Bio::LocatableSeq::new > /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 > STACK: Bio::Seq::Meta::Array::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 > STACK: Bio::Seq::Quality::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 > STACK: Bio::Seq::SeqFactory::create > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 > STACK: Bio::SeqIO::fastq::next_seq > /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 > STACK: fastQParser.pl:12 > > > > On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> Another case for the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi >> >> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >> $seqqual->seq to get the sequence as a string. >> >> Cheers. >> Roy. >> >> On 27/07/2010 15:10, Alan Twaddle wrote: >>> >>> Hello, >>> >>> I am curious as to how I am supposed to use SeqIO::fastq to read >>> in a fastq file and then obtain the nucleotide sequence from that. I >>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>> seen a method within that module that returns the nucleotide sequence. >>> Please, let me know if you have any suggestions! >>> >>> Thank you very much!! >>> >> >> > > > From twaddlac at gmail.com Tue Jul 27 10:55:58 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:55:58 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EF22D.6050705@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: I'm not certain that I'm using the latest BioPerl, but I can check. In the mean time, I'll send you the example data! @FQ4HLCS02EO12Q region=2 tag=H +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII @FQ4HLCS02EO12T region=2 tag=B +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: > Hi Alan, > > It sounds like there's a problem with reading in your Fastq file. Are you > using the latest BioPerl version? There have been many bug fixes to > Bio::SeqIO::fastq over the last couple of years. If you are using an > up-to-date BioPerl, please could you send an example Fastq entry which gives > the error messages? > > Roy. > > On 27/07/2010 15:37, Alan Twaddle wrote: >> >> Whenever I try to access the sequence I get the following error message: >> >> >> --------------------- WARNING --------------------- >> MSG: Seq/Qual descriptions don't match; using sequence description >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: Fastq sequence/quality data length mismatch error >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >> --------------------------------------------------- >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Attempting to set the sequence to >> >> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >> which does not look healthy >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >> STACK: Bio::PrimarySeq::seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >> STACK: Bio::PrimarySeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >> STACK: Bio::LocatableSeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >> STACK: Bio::Seq::Meta::Array::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >> STACK: Bio::Seq::Quality::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >> STACK: Bio::Seq::SeqFactory::create >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >> STACK: Bio::SeqIO::fastq::next_seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >> STACK: fastQParser.pl:12 >> >> >> >> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >> ?wrote: >>> >>> Hi Alan, >>> >>> Another case for the deobfuscator: >>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>> $seqqual->seq to get the sequence as a string. >>> >>> Cheers. >>> Roy. >>> >>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>> >>>> Hello, >>>> >>>> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>> seen a method within that module that returns the nucleotide sequence. >>>> Please, let me know if you have any suggestions! >>>> >>>> Thank you very much!! >>>> >>> >>> >> >> >> > > -- Alan Twaddle, B.S. MUC class of 2010 From biopython at maubp.freeserve.co.uk Tue Jul 27 11:34:11 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Jul 2010 16:34:11 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > Hopefully this is just an email problem, but that doesn't look like a well formatted FASTQ record to me. Where is the "+" line separating the sequence and qualities? Maybe sending this single record as an attachment would work better (is that encouraged on this mailing list?). Peter From roy.chaudhuri at gmail.com Tue Jul 27 11:35:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 16:35:49 +0100 Subject: [Bioperl-l] Fwd: Re: How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: <4C4EFCD5.3030809@gmail.com> Forgot to cc the list: -------- Original Message -------- Subject: Re: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Date: Tue, 27 Jul 2010 16:03:53 +0100 From: Roy Chaudhuri To: Alan Twaddle That doesn't look like Fastq format as defined here: http://nar.oxfordjournals.org/cgi/content/full/gkp1137v1 http://en.wikipedia.org/wiki/FASTQ_format It shouldn't be difficult to write a script to parse it or convert to standard Fastq, though. > p.s. how do I find out what version of bioperl I'm using? http://www.bioperl.org/wiki/FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F On 27/07/2010 15:55, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > > > On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> It sounds like there's a problem with reading in your Fastq file. Are you >> using the latest BioPerl version? There have been many bug fixes to >> Bio::SeqIO::fastq over the last couple of years. If you are using an >> up-to-date BioPerl, please could you send an example Fastq entry which gives >> the error messages? >> >> Roy. >> >> On 27/07/2010 15:37, Alan Twaddle wrote: >>> >>> Whenever I try to access the sequence I get the following error message: >>> >>> >>> --------------------- WARNING --------------------- >>> MSG: Seq/Qual descriptions don't match; using sequence description >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: Fastq sequence/quality data length mismatch error >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >>> --------------------------------------------------- >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Attempting to set the sequence to >>> >>> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >>> which does not look healthy >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >>> STACK: Bio::PrimarySeq::seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >>> STACK: Bio::PrimarySeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >>> STACK: Bio::LocatableSeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >>> STACK: Bio::Seq::Meta::Array::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >>> STACK: Bio::Seq::Quality::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >>> STACK: Bio::Seq::SeqFactory::create >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >>> STACK: Bio::SeqIO::fastq::next_seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >>> STACK: fastQParser.pl:12 >>> >>> >>> >>> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >>> wrote: >>>> >>>> Hi Alan, >>>> >>>> Another case for the deobfuscator: >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>>> $seqqual->seq to get the sequence as a string. >>>> >>>> Cheers. >>>> Roy. >>>> >>>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>>> >>>>> Hello, >>>>> >>>>> I am curious as to how I am supposed to use SeqIO::fastq to read >>>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>>> seen a method within that module that returns the nucleotide sequence. >>>>> Please, let me know if you have any suggestions! >>>>> >>>>> Thank you very much!! >>>>> >>>> >>>> >>> >>> >>> >> >> > > > From cjfields at illinois.edu Tue Jul 27 11:57:43 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 10:57:43 -0500 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <41845A39-5F63-434A-92E6-86C4CA44C89B@illinois.edu> On Jul 27, 2010, at 10:34 AM, Peter wrote: > On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: >> I'm not certain that I'm using the latest BioPerl, but I can check. In >> the mean time, I'll send you the example data! >> >> @FQ4HLCS02EO12Q region=2 tag=H >> +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC >> +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII >> @FQ4HLCS02EO12T region=2 tag=B >> +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC >> +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 >> > > Hopefully this is just an email problem, but that doesn't look like a > well formatted > FASTQ record to me. Where is the "+" line separating the sequence and qualities? > > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). > > Peter As long as the attachment isn't many MB in size, I don't have a problem. Might get delayed by any spam filters though. chris From David.Messina at sbc.su.se Tue Jul 27 12:18:17 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 27 Jul 2010 10:18:17 -0600 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). Absolutely, please try resending as an attachment, Alan. Dave From david.breimann at gmail.com Sat Jul 24 02:47:43 2010 From: david.breimann at gmail.com (David B) Date: Fri, 23 Jul 2010 23:47:43 -0700 (PDT) Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date Message-ID: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Hi, I'm a bit confused about what is the best way to install and maintain the latest updates for bio perl (I'm working on linux). "Installing Bioperl for Unix" (http://www.bioperl.org/wiki/ Installing_Bioperl_for_Unix) suggests using Build.PL or CPAN, but then again I also know that bioperl is currently developed using github (although I know very little about github). 1. Is installing from github an alternative to Build.pL/CPAN options? 2. Does installing from github simply mean cloning than adding the path to PERL5LIB? That's it? 3. I want to use bp_genbank2gff3.pl for circular genomes and I was told I'd better use the developers release of bioperl because only it handles circular genomes correctly. Does it mean I need to clone ...- dev instead of -live and replace the path accordingly? Thanks, David From david.breimann at gmail.com Sat Jul 24 04:06:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sat, 24 Jul 2010 11:06:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl Message-ID: Hello, I'm trying to convert some genbank files downloaded from NCBI to GFF3 format but I keep getting error messages. My bioperl version (according to perl -MBio::Perl -le 'print Bio::Perl->VERSION;') is 1.0069 (I use github live branch). For example, I am trying to convert CP000249.gbk (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk): $ bp_genbank2gff3.pl CP000249.gbk # Input: CP000249.gbk # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia sp. CcI3, complete genome. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: must be scalar or CODE ref STACK: Error::throw STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/Root.pm:473 STACK: Bio::SeqFeature::Tools::TypeMapper::map_types /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 STACK: /usr/local/bin/bp_genbank2gff3.pl:411 ----------------------------------------------------------- Thanks, David From sc.ncrna at gmail.com Sun Jul 25 09:56:02 2010 From: sc.ncrna at gmail.com (ncRNA) Date: Sun, 25 Jul 2010 06:56:02 -0700 (PDT) Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination Message-ID: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Hi all, I am new to this forum and bioperl. I have a list of mouse genomic regions and would like to get the "corresponding" human genomic sequences, which can be seen from the comparative genomics tracks in the UCSC genome browser. Does anyone have any clue on how to realize this? Thanks in advance, ncRNA From twaddlac at gmail.com Tue Jul 27 12:36:43 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 12:36:43 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: Here's some of the data I would like to parse; the entire file was too big to send via email. Also, if there is some problem with the data, I would appreciate any scripting advice since I am unfortunately a noob :-/ Let me know what you think! Thank you all very much! On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >> Maybe sending this single record as an attachment would work better (is that >> encouraged on this mailing list?). > > Absolutely, please try resending as an attachment, Alan. > > > Dave > > -- Alan Twaddle, B.S. MUC class of 2010 -------------- next part -------------- A non-text attachment was scrubbed... Name: exampleData.fastq Type: application/octet-stream Size: 5510 bytes Desc: not available URL: From cjfields at illinois.edu Tue Jul 27 12:55:26 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 11:55:26 -0500 Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination In-Reply-To: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> References: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Message-ID: <2F614027-844E-43EA-8C01-D7C5C7EBF5E5@illinois.edu> Look at the ensembl API for this (I think compara in particular). chris On Jul 25, 2010, at 8:56 AM, ncRNA wrote: > Hi all, > > I am new to this forum and bioperl. I have a list of mouse genomic > regions and would like to get the "corresponding" human genomic > sequences, which can be seen from the comparative genomics tracks in > the UCSC genome browser. Does anyone have any clue on how to realize > this? > > Thanks in advance, > ncRNA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Tue Jul 27 13:14:48 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 18:14:48 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: <4C4F1408.3090707@gmail.com> Hi Alan, It looks like there wasn't any problem with the earlier e-mail, and that your file is not Fastq, but rather some unusual Fastq-like format - where did you get the file from? Here's a one-liner to convert your file into standard Fastq: perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < exampleData.fastq > standard.fastq I've assumed that your sequences and qualities are all single-line with a + prefix. Once you have a standard Fastq file you should be able to parse it with BioPerl. Roy. On 27/07/2010 17:36, Alan Twaddle wrote: > Here's some of the data I would like to parse; the entire file was too > big to send via email. Also, if there is some problem with the data, I > would appreciate any scripting advice since I am unfortunately a noob > :-/ > > Let me know what you think! > > Thank you all very much! > > On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >>> Maybe sending this single record as an attachment would work better (is that >>> encouraged on this mailing list?). >> >> Absolutely, please try resending as an attachment, Alan. >> >> >> Dave >> >> > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From twaddlac at gmail.com Tue Jul 27 14:57:16 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 14:57:16 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4F1408.3090707@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> <4C4F1408.3090707@gmail.com> Message-ID: Ahh thank you very much, everyone!!!! The data was from a GS-FLX Titanium sequencer but it was parsed out of a database into the format that was the "incorrect" fastq style. However, the script worked (though I'm not confident I understand what it just did) and I have successfully parsed the data out of it via BioPerl! Thanks again!! On Tue, Jul 27, 2010 at 1:14 PM, Roy Chaudhuri wrote: > Hi Alan, > > It looks like there wasn't any problem with the earlier e-mail, and that > your file is not Fastq, but rather some unusual Fastq-like format - where > did you get the file from? > > Here's a one-liner to convert your file into standard Fastq: > > perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < > exampleData.fastq > standard.fastq > > I've assumed that your sequences and qualities are all single-line with a + > prefix. > > Once you have a standard Fastq file you should be able to parse it with > BioPerl. > > Roy. > > On 27/07/2010 17:36, Alan Twaddle wrote: >> >> Here's some of the data I would like to parse; the entire file was too >> big to send via email. Also, if there is some problem with the data, I >> would appreciate any scripting advice since I am unfortunately a noob >> :-/ >> >> Let me know what you think! >> >> Thank you all very much! >> >> On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina >> ?wrote: >>>> >>>> Maybe sending this single record as an attachment would work better (is >>>> that >>>> encouraged on this mailing list?). >>> >>> Absolutely, please try resending as an attachment, Alan. >>> >>> >>> Dave >>> >>> >> >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Alan Twaddle, B.S. MUC class of 2010 From cjm at berkeleybop.org Tue Jul 27 18:14:00 2010 From: cjm at berkeleybop.org (Chris Mungall) Date: Tue, 27 Jul 2010 15:14:00 -0700 Subject: [Bioperl-l] bp_genbank2gff3.pl In-Reply-To: References: Message-ID: Hi David I can't replicate this, but I just pushed a change that gives more informative error messages on the 'circular' branch (same branch I pushed the unflattener temp fix for circular genomes) On Jul 24, 2010, at 1:06 AM, David Breimann wrote: > Hello, > > I'm trying to convert some genbank files downloaded from NCBI to GFF3 > format but I keep getting error messages. > > My bioperl version (according to perl -MBio::Perl -le 'print > Bio::Perl->VERSION;') is 1.0069 (I use github live branch). > > For example, I am trying to convert CP000249.gbk > (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk > ): > > $ bp_genbank2gff3.pl CP000249.gbk > # Input: CP000249.gbk > # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia > sp. CcI3, complete genome. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: must be scalar or CODE ref > STACK: Error::throw > STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/ > Root.pm:473 > STACK: Bio::SeqFeature::Tools::TypeMapper::map_types > /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 > STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 > STACK: /usr/local/bin/bp_genbank2gff3.pl:411 > ----------------------------------------------------------- > > Thanks, > David > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lairdm at sfu.ca Tue Jul 27 19:55:08 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 16:55:08 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ Message-ID: <4C4F71DC.7090503@sfu.ca> Good day, Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? Unfortunately the + sign in the name makes it a little hard to google. :) Thanks. From cjfields at illinois.edu Tue Jul 27 21:29:52 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 20:29:52 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4F71DC.7090503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> Message-ID: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > Good day, > > Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? > > Unfortunately the + sign in the name makes it a little hard to google. :) > > Thanks. Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: http://www.bioperl.org/wiki/HOWTO:BlastPlus chris From maj at fortinbras.us Wed Jul 28 00:51:03 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 28 Jul 2010 00:51:03 -0400 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <9BBF74930A5B477FACC15A4E72E98679@NewLife> >is not backward compatible with StandAloneBlast code, which is a feature, not a >bug ;> If that's not the nicest thing anyone's ever said.... ----- Original Message ----- From: "Chris Fields" To: "Matthew Laird" Cc: Sent: Tuesday, July 27, 2010 9:29 PM Subject: Re: [Bioperl-l] StandAloneBlast & BLAST+ > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the >> docs, and based on my quick testing the answer appears to be no, but does >> Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ > (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and > am trying to get our cluster switched over to it as well. It is not backward > compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get > the github version for this. There is also a bit of online documentation on > this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From lairdm at sfu.ca Wed Jul 28 01:14:05 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 22:14:05 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <4C4FBC9D.2020503@sfu.ca> Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... Thanks for the work guys, we couldn't do it without Bioperl at the core. On 10-07-27 06:29 PM, Chris Fields wrote: > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris From dan.bolser at gmail.com Wed Jul 28 05:59:39 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 10:59:39 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 27 July 2010 14:45, Scott Cain wrote: > Hi Dan, > > You might find the deobfuscator helpful: > > ?http://bioperl.org/cgi-bin/deob_interface.cgi I've tried to use that, but I don't understand how to get it to list the objects that implement a certain interface. > Scott > > > On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: >> On 26 July 2010 16:35, Scott Cain wrote: >>> Hi Dan, >>> >>> I think there are probably several BioPerl classes that implement >>> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >>> for? >> >> A way to find what implements what... something like javadoc for bp. >> >> Really I'm looking for a nice 'ontology' of SeqFeatures. >> >> I was thinking that Contig.pm should implement Bio::SeqFeatureI. >> >> >>> Scott >>> >>> >>> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>>> Which objects implement SeqFeatureI, and how should I find that info? >>>> >>>> Sorry for the gratuitous noobs. >>>> >>>> Cheers, >>>> Dan. >>>> _______________________________________________ >>>> 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 >>> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net > GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 > Ontario Institute for Cancer Research > From dan.bolser at gmail.com Wed Jul 28 06:07:38 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 11:07:38 +0100 Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date In-Reply-To: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> References: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Message-ID: On 24 July 2010 07:47, David B wrote: > Hi, > 1. Is installing from github an alternative to Build.pL/CPAN options? Yes, see this page: http://www.bioperl.org/wiki/Using_Git > 2. Does installing from github simply mean cloning than adding the > path to PERL5LIB? That's it? You could do that, or you could apply 'the mantra': perl Build.PL ./Build test ./Build install Don't forget to complain about all failed tests to the appropriate maintainers. > 3. I want to use bp_genbank2gff3.pl for circular genomes and I was > told I'd better use the developers release of bioperl because only it > handles circular genomes correctly. Does it mean I need to clone ...- > dev instead of -live and replace the path accordingly? AFAICT, bioperl-live is "the developers release". Just don't install "bioperl-dead" ... that's really, really bad. > Thanks, > David > > _______________________________________________ > 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 Jul 28 08:56:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 07:56:41 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4FBC9D.2020503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> <4C4FBC9D.2020503@sfu.ca> Message-ID: <397C1B19-0924-4836-B56F-026779E50943@illinois.edu> I'll be working on a 1.6.2 release very soon (had a slight delay due to problems with circular seqs). But BioPerl-Run and others will also be released as well. On Jul 28, 2010, at 12:14 AM, Matthew Laird wrote: > Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? > > I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... > > Thanks for the work guys, we couldn't do it without Bioperl at the core. > > On 10-07-27 06:29 PM, Chris Fields wrote: >> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: >> >>> Good day, >>> >>> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >>> >>> Unfortunately the + sign in the name makes it a little hard to google. :) >>> >>> Thanks. >> >> Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> >> >> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: >> >> http://www.bioperl.org/wiki/HOWTO:BlastPlus >> >> chris From cjfields at illinois.edu Wed Jul 28 09:33:33 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 08:33:33 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > On 27 July 2010 14:45, Scott Cain wrote: >> Hi Dan, >> >> You might find the deobfuscator helpful: >> >> http://bioperl.org/cgi-bin/deob_interface.cgi > > I've tried to use that, but I don't understand how to get it to list > the objects that implement a certain interface. The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. chris From pengyu.ut at gmail.com Wed Jul 28 18:14:33 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 17:14:33 -0500 Subject: [Bioperl-l] Download sequence by genomic location Message-ID: I could download a sequence by location at genome browser. http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 I know that there are ways to get the sequence. But I don't see a way to get the sequence by location. Could anybody let me know if there is such a function in bioperl? http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database -- Regards, Peng From cjfields at illinois.edu Wed Jul 28 18:39:07 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:39:07 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Not for UCSC (IIRC they specifically requested that we not set this functionality up in case their servers were hit too often). I think Galaxy does this, though, and of course you have EntrezGene and the Ensembl API as alternatives. Might be worth re-checking with the UCSC folks to see what their take is on this now... chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 18:47:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:47:08 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Forgot completely, but this should be possible via Bio::DAS: http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm I have used it myself via GBrowse. chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 18:54:44 2010 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 28 Jul 2010 18:54:44 -0400 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: On Wed, Jul 28, 2010 at 6:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database Hi, Peng. You could use the DAS API at the UCSC browser: http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=1:1,1000 The DAS spec is here: http://www.biodas.org/documents/spec-1.53.html And the UCSC FAQ entry is here: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 You could also download the chromosome files from UCSC and then use a FASTA indexing module from bioperl to allow quick random access to the files. I know you are also an R user, so you could use the BSgenome package and the appropriate genome to do the same thing. Sean From pengyu.ut at gmail.com Wed Jul 28 23:40:14 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 22:40:14 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: I didn't see a document for Bio::Das in my bioperl, $ perldoc Bio::Das No documentation found for "Bio::Das". $ perldoc Bio::Das::SegmentI $ perldoc Bio::Das::FeatureTypeI I thought that maybe my bioperl installation is corrupted. Then I install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I install it by "cpan -f Bio::Das". I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the example. It seems that the there is still something missing. I guess there must be some problem with my bioperl installation. Shall I reinstall it? Is there an easy fix? $ ./main.pl Using password in unencrypted URI against RFC #2396 recommendation at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm line 331. Must have IO::Socket::SSL installed to use https: urls: Can't locate Net/SSLeay.pm in @INC (@INC contains: /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. BEGIN failed--compilation aborted at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. Compilation failed in require at (eval 41) line 3. at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm line 200 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new(5); # timeout of 5 sec my @response = $das->dsn('http://stein.cshl.org/perl/das', 'http://genome.cse.ucsc.edu/cgi-bin/das', 'http://user:pass at www.wormbase.org/db/das', 'https://euclid.well.ox.ac.uk/cgi-bin/das', ); for my $url (@response) { if ($url->is_success) { my @dsns = $url->results; print "$url:\t\n"; foreach (@dsns) { print "\t",$_->url,"\t",$_->description,"\n"; } } else { print "$url: ",$url->error,"\n"; } } On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: > Forgot completely, but this should be possible via Bio::DAS: > > http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm > > I have used it myself via GBrowse. > > chris > > On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > >> I could download a sequence by location at genome browser. >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >> >> I know that there are ways to get the sequence. But I don't see a way >> to get the sequence by location. Could anybody let me know if there is >> such a function in bioperl? >> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >> >> -- >> Regards, >> Peng >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Regards, Peng From cjfields at illinois.edu Thu Jul 29 00:46:56 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 23:46:56 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: It's not part of BioPerl, but is on CPAN: http://search.cpan.org/dist/Bio-Das/ You don't appear to be following the Bio::Das API. The following worked for me: #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new( -source => 'http://genome.cse.ucsc.edu/cgi-bin/das', -dsn => 'hg18', ); my $segment = $das->segment('1:1,100000'); for my $sf ($segment->features) { printf("%s(%s):%d-%d(%d)\n", $sf->display_name, $sf->primary_tag, $sf->start, $sf->end, $sf->strand); } chris On Jul 28, 2010, at 10:40 PM, Peng Yu wrote: > I didn't see a document for Bio::Das in my bioperl, > > $ perldoc Bio::Das > No documentation found for "Bio::Das". > $ perldoc Bio::Das::SegmentI > $ perldoc Bio::Das::FeatureTypeI > > I thought that maybe my bioperl installation is corrupted. Then I > install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I > install it by "cpan -f Bio::Das". > > I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the > example. It seems that the there is still something missing. I guess > there must be some problem with my bioperl installation. > > Shall I reinstall it? Is there an easy fix? > > $ ./main.pl > Using password in unencrypted URI against RFC #2396 recommendation at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm > line 331. > Must have IO::Socket::SSL installed to use https: urls: Can't locate > Net/SSLeay.pm in @INC (@INC contains: > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > BEGIN failed--compilation aborted at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > Compilation failed in require at (eval 41) line 3. > at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm > line 200 > > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::Das; > > my $das = Bio::Das->new(5); # timeout of 5 sec > my @response = $das->dsn('http://stein.cshl.org/perl/das', > 'http://genome.cse.ucsc.edu/cgi-bin/das', > 'http://user:pass at www.wormbase.org/db/das', > 'https://euclid.well.ox.ac.uk/cgi-bin/das', > ); > > for my $url (@response) { > if ($url->is_success) { > my @dsns = $url->results; > print "$url:\t\n"; > foreach (@dsns) { > print "\t",$_->url,"\t",$_->description,"\n"; > } > } else { > print "$url: ",$url->error,"\n"; > } > } > > > On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: >> Forgot completely, but this should be possible via Bio::DAS: >> >> http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm >> >> I have used it myself via GBrowse. >> >> chris >> >> On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: >> >>> I could download a sequence by location at genome browser. >>> >>> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >>> >>> I know that there are ways to get the sequence. But I don't see a way >>> to get the sequence by location. Could anybody let me know if there is >>> such a function in bioperl? >>> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >>> >>> -- >>> Regards, >>> Peng >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > > -- > Regards, > Peng > _______________________________________________ > 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 Thu Jul 29 04:08:46 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 09:08:46 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 28 July 2010 14:33, Chris Fields wrote: > On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > >> On 27 July 2010 14:45, Scott Cain wrote: >>> Hi Dan, >>> >>> You might find the deobfuscator helpful: >>> >>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >> >> I've tried to use that, but I don't understand how to get it to list >> the objects that implement a certain interface. > > The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. OK, so at least I'm not being totally dumb when I can't find this info easily... I'll see if I can script it and add the results to the wiki. > chris From cjfields at illinois.edu Thu Jul 29 09:15:11 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jul 2010 08:15:11 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > On 28 July 2010 14:33, Chris Fields wrote: >> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >> >>> On 27 July 2010 14:45, Scott Cain wrote: >>>> Hi Dan, >>>> >>>> You might find the deobfuscator helpful: >>>> >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> I've tried to use that, but I don't understand how to get it to list >>> the objects that implement a certain interface. >> >> The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. > > OK, so at least I'm not being totally dumb when I can't find this info > easily... I'll see if I can script it and add the results to the wiki. > > >> chris Or, better yet, add it to the /scripts or /examples directory for bioperl-live. Code on the wiki can tend to get lost unless it's in a very accessible place. chris From james-platt at hotmail.co.uk Thu Jul 29 10:18:13 2010 From: james-platt at hotmail.co.uk (James) Date: Thu, 29 Jul 2010 07:18:13 -0700 (PDT) Subject: [Bioperl-l] Newbie question installing on MacOSX Message-ID: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Sorry for the newbie question. I am having trouble installing Bioperl. I'm on MacOSX 10.5.8. I downloaded and installed fink: $ fink --version Package manager version: 0.27.13 Distribution version: 0.9.0 i386 I then downloaded Bioperl-1.6.1, I'm trying to install it from source, as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have Xcode installed etc. '# fink install bioperl-pmXXX' I try this: BioPerl-1.6.1 James$ fink install BioPerl-pm Information about 2521 packages read in 1 seconds. Failed: no package found for specification 'BioPerl-pm'! The version of perl I'm running is 5.8.8, I have tried 'fink install BioPerl588' but this doesn't work either. Thanks very much, James From awitney at sgul.ac.uk Thu Jul 29 11:06:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Thu, 29 Jul 2010 16:06:01 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <08188444-D800-43FD-B1BB-4E1B4332BB46@sgul.ac.uk> Hi James, You are mixing up your installation methods. Either install with fink, or download the source and install from there, not both. I would personally recommend installing it from source or better still install from cpan. Take a look here: http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_Build.PL http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN If you really want to use fink then take a look here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink It looks like the command for this is: fink install bioperl-pm588 but I don't use fink any more so I am not certain of how that works. adam On 29 Jul 2010, at 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 11:23:06 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:23:06 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <4C519CDA.8010008@gmail.com> Hi James, I don't know anything about Macs, but looking here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink shouldn't the command be "fink install bioperl-pm588"? Roy. On 29/07/2010 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 11:36:11 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:36:11 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> Message-ID: <4C519FEB.8050702@gmail.com> Please copy replies to the mailing list, that way others can respond. Try the command: perl -MBio::Seq -e '' If Bioperl is not installed you will get an error message starting "Can't locate Bio/Seq in @INC". If the command just exits silently then BioPerl is installed correctly. Roy. On 29/07/2010 16:29, James Platt wrote: > Hi, > > I tried that, sorry I wasn't clear in the first post. > > James$ fink install bioperl-pm588 > Information about 2521 packages read in 0 seconds. > Failed: no package found for specification 'bioperl-pm588'! > > I think I may have installed it through fink commander. how do i check > in unix that it is in fact installed? > > Thanks, > > James > > On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: > >> Hi James, >> >> I don't know anything about Macs, but looking here: >> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >> >> shouldn't the command be "fink install bioperl-pm588"? >> >> Roy. >> >> On 29/07/2010 15:18, James wrote: >>> Sorry for the newbie question. >>> >>> I am having trouble installing Bioperl. >>> >>> I'm on MacOSX 10.5.8. >>> >>> I downloaded and installed fink: >>> >>> $ fink --version >>> Package manager version: 0.27.13 >>> Distribution version: 0.9.0 i386 >>> >>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>> source, >>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>> Xcode installed etc. >>> >>> '# fink install bioperl-pmXXX' >>> >>> I try this: >>> >>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>> >>> Information about 2521 packages read in 1 seconds. >>> Failed: no package found for specification 'BioPerl-pm'! >>> >>> >>> The version of perl I'm running is 5.8.8, I have tried 'fink install >>> BioPerl588' but this doesn't work either. >>> >>> Thanks very much, >>> >>> James >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From james-platt at hotmail.co.uk Thu Jul 29 12:11:48 2010 From: james-platt at hotmail.co.uk (James Platt) Date: Thu, 29 Jul 2010 17:11:48 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <4C519FEB.8050702@gmail.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> <4C519FEB.8050702@gmail.com> Message-ID: when I'm in the directory it exits silently. When I'm not... James$ perl -MBio::Seq -e '' Can't locate Bio/Seq.pm in @INC (@INC contains: /sw/lib/perl5/darwin- thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/ Updates/5.8.8 /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 .). BEGIN failed--compilation aborted. I guess I need to try install it again. J On 29 Jul 2010, at 16:36, Roy Chaudhuri wrote: > Please copy replies to the mailing list, that way others can respond. > > Try the command: > perl -MBio::Seq -e '' > > If Bioperl is not installed you will get an error message starting > "Can't locate Bio/Seq in @INC". If the command just exits silently > then BioPerl is installed correctly. > > Roy. > > On 29/07/2010 16:29, James Platt wrote: >> Hi, >> >> I tried that, sorry I wasn't clear in the first post. >> >> James$ fink install bioperl-pm588 >> Information about 2521 packages read in 0 seconds. >> Failed: no package found for specification 'bioperl-pm588'! >> >> I think I may have installed it through fink commander. how do i >> check >> in unix that it is in fact installed? >> >> Thanks, >> >> James >> >> On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: >> >>> Hi James, >>> >>> I don't know anything about Macs, but looking here: >>> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >>> >>> shouldn't the command be "fink install bioperl-pm588"? >>> >>> Roy. >>> >>> On 29/07/2010 15:18, James wrote: >>>> Sorry for the newbie question. >>>> >>>> I am having trouble installing Bioperl. >>>> >>>> I'm on MacOSX 10.5.8. >>>> >>>> I downloaded and installed fink: >>>> >>>> $ fink --version >>>> Package manager version: 0.27.13 >>>> Distribution version: 0.9.0 i386 >>>> >>>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>>> source, >>>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>>> Xcode installed etc. >>>> >>>> '# fink install bioperl-pmXXX' >>>> >>>> I try this: >>>> >>>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>>> >>>> Information about 2521 packages read in 1 seconds. >>>> Failed: no package found for specification 'BioPerl-pm'! >>>> >>>> >>>> The version of perl I'm running is 5.8.8, I have tried 'fink >>>> install >>>> BioPerl588' but this doesn't work either. >>>> >>>> Thanks very much, >>>> >>>> James >>>> >>>> _______________________________________________ >>>> 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 Thu Jul 29 14:17:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 19:17:42 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 29 July 2010 14:15, Chris Fields wrote: > On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > >> On 28 July 2010 14:33, Chris Fields wrote: >>> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >>> >>>> On 27 July 2010 14:45, Scott Cain wrote: >>>>> Hi Dan, >>>>> >>>>> You might find the deobfuscator helpful: >>>>> >>>>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> I've tried to use that, but I don't understand how to get it to list >>>> the objects that implement a certain interface. >>> >>> The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. >> >> OK, so at least I'm not being totally dumb when I can't find this info >> easily... I'll see if I can script it and add the results to the wiki. >> >> >>> chris > > Or, better yet, add it to the /scripts or /examples directory for bioperl-live. ?Code on the wiki can tend to get lost unless it's in a very accessible place. I meant I'd add the results to the wiki. Nice idea to add the code to the distro. > chris From frederic.romagne at gmail.com Fri Jul 30 00:59:35 2010 From: frederic.romagne at gmail.com (=?ISO-8859-1?Q?Fr=E9d=E9ric_Romagn=E9?=) Date: Fri, 30 Jul 2010 14:59:35 +1000 Subject: [Bioperl-l] phyloxml and element order Message-ID: Hi, I'm using bioperl to create phyloxml trees, after few tentatives, i got my tree with all the element/attributes i want but when I write the tree, element are not written following the order specified in the XSD Schema. For example, i got : Loxosceles intermedia Araneomorphae Sicariidae 969 HAAERADSRKPIWDIAHMVNDLELVD Araneomorphae Sicariidae The program forester complains that should be written before the element. According to http://phyloxml.wordpress.com/2009/11/25/order-of-elements-in-phyloxml this is what bioperl is supposed to do. All my element/attributes are set before writing the tree using 'add_Annotation', 'add_tag_value' and 'sequence' methods from a Bio::Tree::AnnotatableNode object, so i think the error comes from the write_tree method. Any help would be appreciated. Thank you, Fred From com505 at york.ac.uk Fri Jul 30 05:37:11 2010 From: com505 at york.ac.uk (Carrie O'Malley) Date: Fri, 30 Jul 2010 10:37:11 +0100 Subject: [Bioperl-l] installing bioperl Message-ID: Hi there I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. I am not able to complete the installation as every time I get: Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have tried using both methods to install into a local folder and get the same thing !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/home/users/carrieomalley/bin' mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( Many thanks in advance Carrie Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: Data::Stag is not installed (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) CPAN: Storable loaded ok (v2.18) Going to read /Users/carrieomalley/.cpan/Metadata Database was generated on Sat, 10 Jul 2010 11:27:04 GMT Running install for module 'Data::Stag' 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok x Data-Stag-0.11/ x Data-Stag-0.11/c-ext/ x Data-Stag-0.11/c-ext/README.c-ext x Data-Stag-0.11/c-ext/staglib.c x Data-Stag-0.11/c-ext/staglib.h x Data-Stag-0.11/Changes x Data-Stag-0.11/Data/ x Data-Stag-0.11/Data/Stag/ x Data-Stag-0.11/Data/Stag/Arr2HTML.pm x Data-Stag-0.11/Data/Stag/Base.pm x Data-Stag-0.11/Data/Stag/BaseGenerator.pm x Data-Stag-0.11/Data/Stag/BaseHandler.pm x Data-Stag-0.11/Data/Stag/ChainHandler.pm x Data-Stag-0.11/Data/Stag/DTDWriter.pm x Data-Stag-0.11/Data/Stag/GraphHandler.pm x Data-Stag-0.11/Data/Stag/HashDB.pm x Data-Stag-0.11/Data/Stag/IndentParser.pm x Data-Stag-0.11/Data/Stag/IndentWriter.pm x Data-Stag-0.11/Data/Stag/ITextParser.pm x Data-Stag-0.11/Data/Stag/ITextWriter.pm x Data-Stag-0.11/Data/Stag/null.pm x Data-Stag-0.11/Data/Stag/PerlWriter.pm x Data-Stag-0.11/Data/Stag/PodParser.pm x Data-Stag-0.11/Data/Stag/SAX2Stag.pm x Data-Stag-0.11/Data/Stag/Simple.pm x Data-Stag-0.11/Data/Stag/StagDB.pm x Data-Stag-0.11/Data/Stag/StagI.pm x Data-Stag-0.11/Data/Stag/StagImpl.pm x Data-Stag-0.11/Data/Stag/SxprParser.pm x Data-Stag-0.11/Data/Stag/SxprWriter.pm x Data-Stag-0.11/Data/Stag/Util.pm x Data-Stag-0.11/Data/Stag/Writer.pm x Data-Stag-0.11/Data/Stag/XMLParser.pm x Data-Stag-0.11/Data/Stag/XMLWriter.pm x Data-Stag-0.11/Data/Stag/XSLHandler.pm x Data-Stag-0.11/Data/Stag/XSLTHandler.pm x Data-Stag-0.11/Data/Stag.pm x Data-Stag-0.11/dev/ x Data-Stag-0.11/dev/create-manifest.sh x Data-Stag-0.11/dev/data-stag.spec x Data-Stag-0.11/dev/mkspec.pl x Data-Stag-0.11/elisp/ x Data-Stag-0.11/elisp/itext-mode.el x Data-Stag-0.11/homepage/ x Data-Stag-0.11/homepage/archBIG.png x Data-Stag-0.11/homepage/dbstag-tutorial.sgml x Data-Stag-0.11/homepage/images/ x Data-Stag-0.11/homepage/images/k-schema-diagram.png x Data-Stag-0.11/homepage/images/rr-schema-diagram.png x Data-Stag-0.11/homepage/index.html x Data-Stag-0.11/homepage/makefile x Data-Stag-0.11/homepage/mk.sh x Data-Stag-0.11/homepage/mkpodhtml.pl x Data-Stag-0.11/homepage/mkscriptdoc.pl x Data-Stag-0.11/homepage/script-docs/ x Data-Stag-0.11/homepage/script-docs/selectall_html.html x Data-Stag-0.11/homepage/script-docs/selectall_xml.html x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html x Data-Stag-0.11/homepage/script-docs/stag-db.html x Data-Stag-0.11/homepage/script-docs/stag-diff.html x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html x Data-Stag-0.11/homepage/script-docs/stag-elcount.html x Data-Stag-0.11/homepage/script-docs/stag-eval.html x Data-Stag-0.11/homepage/script-docs/stag-filter.html x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html x Data-Stag-0.11/homepage/script-docs/stag-flatten.html x Data-Stag-0.11/homepage/script-docs/stag-grep.html x Data-Stag-0.11/homepage/script-docs/stag-handle.html x Data-Stag-0.11/homepage/script-docs/stag-ir.html x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html x Data-Stag-0.11/homepage/script-docs/stag-join.html x Data-Stag-0.11/homepage/script-docs/stag-merge.html x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html x Data-Stag-0.11/homepage/script-docs/stag-parse.html x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html x Data-Stag-0.11/homepage/script-docs/stag-query.html x Data-Stag-0.11/homepage/script-docs/stag-show-template.html x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html x Data-Stag-0.11/homepage/script-docs/stag-splitter.html x Data-Stag-0.11/homepage/script-docs/stag-storenode.html x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html x Data-Stag-0.11/homepage/script-docs/stag-view.html x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html x Data-Stag-0.11/homepage/script-list.html x Data-Stag-0.11/homepage/stag-db-tutorial.html x Data-Stag-0.11/homepage/stag-poster.html x Data-Stag-0.11/INSTALL x Data-Stag-0.11/Makefile.PL x Data-Stag-0.11/MANIFEST x Data-Stag-0.11/META.yml x Data-Stag-0.11/README x Data-Stag-0.11/scripts/ x Data-Stag-0.11/scripts/stag-autoschema.pl x Data-Stag-0.11/scripts/stag-db.pl x Data-Stag-0.11/scripts/stag-diff.pl x Data-Stag-0.11/scripts/stag-drawtree.pl x Data-Stag-0.11/scripts/stag-elcount.pl x Data-Stag-0.11/scripts/stag-eval.pl x Data-Stag-0.11/scripts/stag-filter.pl x Data-Stag-0.11/scripts/stag-findsubtree.pl x Data-Stag-0.11/scripts/stag-flatten.pl x Data-Stag-0.11/scripts/stag-grep.pl x Data-Stag-0.11/scripts/stag-handle.pl x Data-Stag-0.11/scripts/stag-itext2simple.pl x Data-Stag-0.11/scripts/stag-itext2sxpr.pl x Data-Stag-0.11/scripts/stag-itext2xml.pl x Data-Stag-0.11/scripts/stag-join.pl x Data-Stag-0.11/scripts/stag-merge.pl x Data-Stag-0.11/scripts/stag-mogrify.pl x Data-Stag-0.11/scripts/stag-parse.pl x Data-Stag-0.11/scripts/stag-query.pl x Data-Stag-0.11/scripts/stag-splitter.pl x Data-Stag-0.11/scripts/stag-view.pl x Data-Stag-0.11/scripts/stag-xml2itext.pl x Data-Stag-0.11/scripts/stag-xmlsplit.pl x Data-Stag-0.11/t/ x Data-Stag-0.11/t/animal.x x Data-Stag-0.11/t/autoschema.t x Data-Stag-0.11/t/barfly.x x Data-Stag-0.11/t/bio.x x Data-Stag-0.11/t/chainhandler.t x Data-Stag-0.11/t/collapse.x x Data-Stag-0.11/t/data/ x Data-Stag-0.11/t/data/attrs.xml x Data-Stag-0.11/t/data/bf.txt x Data-Stag-0.11/t/data/eco.el x Data-Stag-0.11/t/data/eco.itext x Data-Stag-0.11/t/data/homol.itext x Data-Stag-0.11/t/data/persons.el x Data-Stag-0.11/t/db.t x Data-Stag-0.11/t/emptytag.t x Data-Stag-0.11/t/get.t x Data-Stag-0.11/t/graph.x x Data-Stag-0.11/t/handlers.t x Data-Stag-0.11/t/handlers2.t x Data-Stag-0.11/t/handlers2.x x Data-Stag-0.11/t/hashdb.t x Data-Stag-0.11/t/hashdb.x x Data-Stag-0.11/t/homol.t x Data-Stag-0.11/t/lisp.x x Data-Stag-0.11/t/parsestr.t x Data-Stag-0.11/t/path.x x Data-Stag-0.11/t/path2.x x Data-Stag-0.11/t/qmatch.t x Data-Stag-0.11/t/roundtrip-attrs.t x Data-Stag-0.11/t/set-attrs.t x Data-Stag-0.11/t/set.t x Data-Stag-0.11/t/sxpr.t x Data-Stag-0.11/t/unhash.t x Data-Stag-0.11/t/unset.t x Data-Stag-0.11/t/write.t x Data-Stag-0.11/t/xml1.t x Data-Stag-0.11/t/xml2.t CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz External Module XML::LibXSLT, XSLT, is not installed on this computer. Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations External Module XML::Parser::PerlSAX, SAX Handler, is not installed on this computer. Data::Stag::XMLParser in Data::Stag needs it for parsing XML External Module GD, Graphical Drawing Toolkit, is not installed on this computer. stag-drawtree.pl in Data::Stag needs it for drawing trees External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer. Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs External Module Tk, Tk, is not installed on this computer. stag-view.pl in Data::Stag needs it for tree viewer Information: There are some external packages and perl modules, listed above, which stag uses. This only effects the functionality which is listed above: the rest of stag will work fine, which includes nearly all of the core functionality. Enjoy the rest of stag, which you can use after going 'make install' Checking if your kit is complete... Looks good Writing Makefile for Data Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm cp Data/Stag.pm blib/lib/Data/Stag.pm cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm cp scripts/stag-view.pl blib/script/stag-view.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl cp scripts/stag-grep.pl blib/script/stag-grep.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl cp scripts/stag-merge.pl blib/script/stag-merge.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl cp scripts/stag-parse.pl blib/script/stag-parse.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl cp scripts/stag-join.pl blib/script/stag-join.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl cp scripts/stag-db.pl blib/script/stag-db.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl cp scripts/stag-filter.pl blib/script/stag-filter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl cp scripts/stag-handle.pl blib/script/stag-handle.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl cp scripts/stag-query.pl blib/script/stag-query.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl cp scripts/stag-flatten.pl blib/script/stag-flatten.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl cp scripts/stag-splitter.pl blib/script/stag-splitter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl cp scripts/stag-diff.pl blib/script/stag-diff.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl Manifying blib/man1/stag-view.pl.1 Manifying blib/man1/stag-mogrify.pl.1 Manifying blib/man1/stag-grep.pl.1 Manifying blib/man1/stag-handle.pl.1 Manifying blib/man1/stag-drawtree.pl.1 Manifying blib/man1/stag-query.pl.1 Manifying blib/man1/stag-merge.pl.1 Manifying blib/man1/stag-parse.pl.1 Manifying blib/man1/stag-findsubtree.pl.1 Manifying blib/man1/stag-join.pl.1 Manifying blib/man1/stag-autoschema.pl.1 Manifying blib/man1/stag-db.pl.1 Manifying blib/man1/stag-flatten.pl.1 Manifying blib/man1/stag-splitter.pl.1 Manifying blib/man1/stag-diff.pl.1 Manifying blib/man1/stag-filter.pl.1 Manifying blib/man3/Data::Stag::StagDB.3pm Manifying blib/man3/Data::Stag::SxprWriter.3pm Manifying blib/man3/Data::Stag.3pm Manifying blib/man3/Data::Stag::ChainHandler.3pm Manifying blib/man3/Data::Stag::IndentParser.3pm Manifying blib/man3/Data::Stag::Simple.3pm Manifying blib/man3/Data::Stag::SAX2Stag.3pm Manifying blib/man3/Data::Stag::Arr2HTML.3pm Manifying blib/man3/Data::Stag::XSLHandler.3pm Manifying blib/man3/Data::Stag::PerlWriter.3pm Manifying blib/man3/Data::Stag::XSLTHandler.3pm Manifying blib/man3/Data::Stag::DTDWriter.3pm Manifying blib/man3/Data::Stag::Writer.3pm Manifying blib/man3/Data::Stag::XMLWriter.3pm Manifying blib/man3/Data::Stag::GraphHandler.3pm Manifying blib/man3/Data::Stag::XMLParser.3pm Manifying blib/man3/Data::Stag::StagImpl.3pm Manifying blib/man3/Data::Stag::PodParser.3pm Manifying blib/man3/Data::Stag::BaseGenerator.3pm Manifying blib/man3/Data::Stag::IndentWriter.3pm Manifying blib/man3/Data::Stag::HashDB.3pm Manifying blib/man3/Data::Stag::null.3pm Manifying blib/man3/Data::Stag::ITextParser.3pm Manifying blib/man3/Data::Stag::BaseHandler.3pm Manifying blib/man3/Data::Stag::ITextWriter.3pm Manifying blib/man3/Data::Stag::SxprParser.3pm CMUNGALL/Data-Stag-0.11.tar.gz make -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/autoschema.........ok t/chainhandler.......ok t/db.................ok t/emptytag...........ok 3/3 skipped: various reasons t/get................ok t/handlers...........ok t/handlers2..........ok 1/9 skipped: various reasons t/hashdb.............ok t/homol..............ok t/parsestr...........ok 6/6 skipped: various reasons t/qmatch.............ok t/roundtrip-attrs....ok 5/5 skipped: various reasons t/set-attrs..........ok 3/3 skipped: various reasons t/set................ok t/sxpr...............ok t/unhash.............ok t/unset..............ok t/write..............ok t/xml1...............ok 7/7 skipped: various reasons t/xml2...............ok 4/4 skipped: various reasons All tests successful, 29 subtests skipped. Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) CMUNGALL/Data-Stag-0.11.tar.gz make test -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make install Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1 make: *** [pure_site_install] Error 13 CMUNGALL/Data-Stag-0.11.tar.gz make install -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state *** (back in Bioperl Build.PL) *** Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n - ERROR: You chose to install Data::Stag but it failed to install * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Spreadsheet::ParseExcel is not installed (wanted for parsing Excel files, used by Bio::SeqIO::excel) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite Graph is not installed (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) * Optional prerequisite SVG::Graph is not installed (wanted for creating SVG images, used by Bio::TreeIO::svggraph) * Optional prerequisite SOAP::Lite is not installed (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Convert::Binary::C is not installed (wanted for strider functionality, used by Bio::SeqIO::strider) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite XML::Twig is not installed (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) * Optional prerequisite Set::Scalar is not installed (wanted for proper operation, used by Bio::Tree::Compatible) * Optional prerequisite XML::Parser::PerlSAX is not installed (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite Clone is not installed (wanted for cloning objects, used by Bio::Tools::Primer3) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: BioDBGFF.................disabled * MySQL, Pg nor Oracle DBI drivers are installed BioDBSeqFeature_mysql....disabled - DBD::mysql is not installed Network..................enabled BioDBSeqFeature_BDB......enabled Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] n - will not run internet-requiring tests Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'BioPerl' version '1.006000' Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok 1/28 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- # Looks like you planned 28 tests but only ran 7. # Looks like your test died just after 7. t/AlignIO/AlignIO............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 8-28 Failed 21/28 tests, 25.00% okay t/AlignIO/arp................................ok 1/48 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- # Looks like you planned 48 tests but only ran 2. # Looks like your test died just after 2. t/AlignIO/arp................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-48 Failed 46/48 tests, 4.17% okay 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......................ok 1/159 # Failed test 'use Bio::Annotation::TagTree;' # at t/Annotation/Annotation.t line 20. # Tried to use 'Bio::Annotation::TagTree'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. # Compilation failed in require at (eval 37) line 2. # BEGIN failed--compilation aborted at (eval 37) line 2. t/Annotation/Annotation......................NOK 9/159 # Failed test 'default itext' # at t/Annotation/Annotation.t line 307. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' # Failed test 'itext' # at t/Annotation/Annotation.t line 315. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. # Looks like you planned 159 tests but only ran 119. # Looks like you failed 3 tests of 119 run. # Looks like your test died just after 119. t/Annotation/Annotation......................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 9, 117, 119-159 Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................ok 1/51 # Failed (TODO) test at t/Assembly/Assembly.t line 35. t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok 1/24 skipped: various reasons t/Biblio/References..........................ok t/Biblio/biofetch............................skipped all skipped: Network tests have not been requested t/Biblio/eutils..............................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/ClusterIO/ClusterIO........................ok 8/12 skipped: various reasons t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/ClusterIO/SequenceFamily.t:16 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. # Looks like you planned 19 tests but only ran 2. # Looks like your test died just after 2. t/ClusterIO/SequenceFamily...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-19 Failed 17/19 tests, 10.53% okay 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 11/279 skipped: various reasons t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 STACK: t/LocalDB/Flat.t:89 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. # Looks like you planned 24 tests but only ran 14. # Looks like your test died just after 14. t/LocalDB/Flat...............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-24 Failed 10/24 tests, 58.33% okay t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 STACK: t/LocalDB/Index.t:91 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. # Looks like you planned 64 tests but only ran 31. # Looks like your test died just after 31. t/LocalDB/Index..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 32-64 Failed 33/64 tests, 48.44% okay t/LocalDB/Registry...........................ok 9/14 skipped: various reasons t/LocalDB/SeqFeature.........................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok 19/267 skipped: various reasons 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 10/14 skipped: various reasons t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok 10/29 skipped: various reasons 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..................................ok t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok 4/46 skipped: various reasons t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................skipped all skipped: Network tests have not been requested t/RemoteDB/CUTG..............................ok 14/37 skipped: various reasons t/RemoteDB/DB................................skipped all skipped: Network tests have not been requested t/RemoteDB/EMBL..............................skipped all skipped: Network tests have not been requested t/RemoteDB/EUtilities........................skipped all skipped: Network tests have not been requested t/RemoteDB/HIV/HIV...........................ok 13/30 skipped: various reasons t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok 10/41 skipped: various reasons t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok 10/16 skipped: various reasons t/RemoteDB/SeqHound..........................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqRead_fail......................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqVersion........................ok 8/10 skipped: various reasons t/RemoteDB/Taxonomy..........................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................ok 1/18 # Failed (TODO) test at t/Restriction/IO.t line 31. t/Restriction/IO.............................ok 3/18 skipped: various reasons t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................ok 2/31 skipped: various reasons t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped all 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.............................ok 1/1093 # Failed (TODO) test at t/SearchIO/blast.t line 527. # '0.852' # > # '0.9' # Failed (TODO) test at t/SearchIO/blast.t line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................ok 1/289 # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................ok 1/298 # Failed (TODO) test at t/SearchIO/blastxml.t line 258. # got: undef # expected: '31984247' # Failed (TODO) test at t/SearchIO/blastxml.t line 259. # got: undef # expected: '88780' # Failed (TODO) test at t/SearchIO/blastxml.t line 260. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok 4/45 skipped: various reasons 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...........................ok 1/116 # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. # got: 'Bio::Location::Simple=HASH(0x100838ce8)' # expected: undef # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test at t/Seq/LocatableSeq.t 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 all 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 all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok 7/214 skipped: various reasons t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqIO/Handler.t:20 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. # Looks like you planned 550 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/Handler..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-550 Failed 549/550 tests, 0.18% okay t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped all 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..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped all skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ # Failed test 'use Bio::SeqIO::chaos;' # at t/SeqIO/chaos.t line 15. # Tried to use 'Bio::SeqIO::chaos'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. # Looks like you failed 1 test of 8. t/SeqIO/chaos................................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/8 tests, 87.50% okay t/SeqIO/chaosxml.............................skipped all skipped: The optional module Data::Stag (or dependencies thereof) was not installed t/SeqIO/ctf..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped all 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 all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................ok 1/17 # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 54. # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped all 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 all 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 all 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..................................ok 1/59 # Failed (TODO) test 'accuracies' # at t/SeqIO/scf.t line 78. # got: 'ARRAY(0x100ac5648)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ # Failed test 'use Bio::SeqIO::swiss;' # at t/SeqIO/swiss.t line 12. # Tried to use 'Bio::SeqIO::swiss'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. # Looks like you planned 240 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqIO/swiss................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-240 Failed 240/240 tests, 0.00% okay t/SeqIO/tab..................................ok t/SeqIO/table................................ok 112/450 skipped: various reasons t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped all 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 1/49Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqTools/GuessSeqFormat.t:62 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time t/SeqTools/GuessSeqFormat....................NOK 25/49 # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. # ' # at t/SeqTools/GuessSeqFormat.t line 71. # got: '0' # expected: '1' # Looks like you planned 49 tests but ran 1 extra. # Looks like you failed 1 test of 50 run. t/SeqTools/GuessSeqFormat....................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED tests 25, 50 Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok 5/21 skipped: various reasons t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped all 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 all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut..............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos.............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/Tools/Analysis/Protein/Scansite.t:23 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. # Looks like you planned 14 tests but only ran 4. # Looks like your test died just after 4. t/Tools/Analysis/Protein/Scansite............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-14 Failed 10/14 tests, 28.57% okay t/Tools/Analysis/Protein/Sopma...............ok 12/16 skipped: various reasons 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 all 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......................skipped all skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast..................ok 12/45 skipped: various reasons 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 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 all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok 2/74 skipped: various reasons t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................ok t/Tree/TreeIO/svggraph.......................ok 3/4 skipped: various reasons 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 15/26 skipped: various reasons Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/AlignIO/AlignIO.t 255 65280 28 42 8-28 t/AlignIO/arp.t 255 65280 48 92 3-48 t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 t/LocalDB/Flat.t 255 65280 24 20 15-24 t/LocalDB/Index.t 255 65280 64 66 32-64 t/SeqIO/Handler.t 255 65280 550 1098 2-550 t/SeqIO/chaos.t 1 256 8 1 1 t/SeqIO/swiss.t 255 65280 240 479 1-240 t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 57 tests and 313 subtests skipped. Failed 11/318 test scripts. 970/17228 subtests failed. Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) Failed 11/318 test programs. 970/17228 subtests failed. Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 From robfsouza at gmail.com Fri Jul 30 09:54:08 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 30 Jul 2010 09:54:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Did you try, as root, ./Build.pl --install_base /opt/local ? Also, check the INSTALL file at the root of the bioperl distribution. Robson On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > ?I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > ?- ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > ?is not installed on this computer. > ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > ?is not installed on this computer. > ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > ?is not installed on this computer. > ?stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > ?is not installed on this computer. > ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > ?is not installed on this computer. > ?stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > ? There are some external packages and perl modules, listed above, which > ? stag uses. This only effects the functionality which is listed above: > ? the rest of stag will work fine, which includes nearly all of the > ? core functionality. > > ? Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > ? ? ? ?3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > ? ? ? ?1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > ? ? ? ?6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > ? ? ? ?5/5 skipped: various reasons > t/set-attrs..........ok > ? ? ? ?3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > ? ? ? ?7/7 skipped: various reasons > t/xml2...............ok > ? ? ? ?4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at -e line 1 > make: *** [pure_site_install] Error 13 > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make install ?-- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > ?- ERROR: You chose to install Data::Stag but it failed to install > ?* Optional prerequisite Ace is not installed > ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > ?* Optional prerequisite Spreadsheet::ParseExcel is not installed > ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) > ?* Optional prerequisite Math::Random is not installed > ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > ?* Optional prerequisite Graph is not installed > ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > ?* Optional prerequisite SVG::Graph is not installed > ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > ?* Optional prerequisite SOAP::Lite is not installed > ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed > ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > ?* Optional prerequisite GraphViz is not installed > ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > ?* Optional prerequisite Array::Compare is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite Convert::Binary::C is not installed > ? (wanted for strider functionality, used by Bio::SeqIO::strider) > ?* Optional prerequisite Algorithm::Munkres is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite XML::Twig is not installed > ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > ?* Optional prerequisite Set::Scalar is not installed > ? (wanted for proper operation, used by Bio::Tree::Compatible) > ?* Optional prerequisite XML::Parser::PerlSAX is not installed > ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > ?* Optional prerequisite XML::SAX::Writer is not installed > ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) > ?* Optional prerequisite Clone is not installed > ? (wanted for cloning objects, used by Bio::Tools::Primer3) > ?* Optional prerequisite XML::DOM::XPath is not installed > ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > ?* Optional prerequisite PostScript::TextBlock is not installed > ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > ?BioDBGFF.................disabled > ? ?* MySQL, Pg nor Oracle DBI drivers are installed > ?BioDBSeqFeature_mysql....disabled > ? ?- DBD::mysql is not installed > ?Network..................enabled > ?BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > ?- will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > ?- will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > ? ? ? ?Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > ? ? ? ?Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # ? Failed test 'use Bio::Annotation::TagTree;' > # ? at t/Annotation/Annotation.t line 20. > # ? ? Tried to use 'Bio::Annotation::TagTree'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # ? Failed test 'default itext' > # ? at t/Annotation/Annotation.t line 307. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > > # ? Failed test 'itext' > # ? at t/Annotation/Annotation.t line 315. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > ? ? ? ?1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > ? ? ? ?8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > ? ? ? ?Failed 17/19 tests, 10.53% okay > 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 > ? ? ? ?11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > ? ? ? ?Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > ? ? ? ?Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > ? ? ? ?9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > ? ? ? ?19/267 skipped: various reasons > 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 > ? ? ? ?10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > ? ? ? ?10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > ? ? ? ?4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > ? ? ? ?14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > ? ? ? ?13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > ? ? ? ?10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > ? ? ? ?10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > ? ? ? ?8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # ? Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > ? ? ? ?3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > ? ? ? ?2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > ? ? ? ?all 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.............................ok 1/1093 > # ? Failed (TODO) test at t/SearchIO/blast.t line 527. > # ? ? '0.852' > # ? ? ? ? > > # ? ? '0.9' > > # ? Failed (TODO) test at t/SearchIO/blast.t line 528. > # ? ? '1.599' > # ? ? ? ? <= > # ? ? '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # ? ? ? ? ?got: '0.946' > # ? ? expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # ? ? ? ? ?got: undef > # ? ? expected: '31984247' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # ? ? ? ? ?got: undef > # ? ? expected: '88780' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # ? ? ? ? ?got: undef > # ? ? expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > ? ? ? ?4/45 skipped: various reasons > 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...........................ok 1/116 > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # ? ? expected: undef > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # ? ? ? ? ?got: '\-\.=~' > # ? ? expected: '-\?' > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > ? ? ? ?7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > ? ? ? ?Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > ? ? ? ?all 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..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # ? Failed test 'use Bio::SeqIO::chaos;' > # ? at t/SeqIO/chaos.t line 15. > # ? ? Tried to use 'Bio::SeqIO::chaos'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > ? ? ? ?Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # ? Failed (TODO) test 'primary_id' > # ? at t/SeqIO/gcg.t line 54. > # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # ? ? expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > ? ? ? ?all 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 > ? ? ? ?all 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 > ? ? ? ?all 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..................................ok 1/59 > # ? Failed (TODO) test 'accuracies' > # ? at t/SeqIO/scf.t line 78. > # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' > # ? ? expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # ? Failed test 'use Bio::SeqIO::swiss;' > # ? at t/SeqIO/swiss.t line 12. > # ? ? Tried to use 'Bio::SeqIO::swiss'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > ? ? ? ?Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > ? ? ? ?112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # ? at t/SeqTools/GuessSeqFormat.t line 71. > # ? ? ? ? ?got: '0' > # ? ? expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > ? ? ? ?5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > ? ? ? ?Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > ? ? ? ?12/16 skipped: various reasons > 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 > ? ? ? ?all 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......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > ? ? ? ?12/45 skipped: various reasons > 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 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 > ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > ? ? ? ?2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > ? ? ? ?3/4 skipped: various reasons > 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 > ? ? ? ?15/26 skipped: various reasons > Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 > t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 > t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 > t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 > t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 > t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 > t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 > t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 > t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 > t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 > t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > 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 Fri Jul 30 11:26:12 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Fri, 30 Jul 2010 16:26:12 +0100 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: <70A35EB0-D004-4B7A-A239-D9EA7F9EA206@sgul.ac.uk> It looks like it is trying to install and failing because of lack of permissions. I would recommend you try the cpan route like this: perl -MCPAN -e shell then from the cpan prompt, set a few things up (only need to do this once): cpan> o conf make_install_make_command 'sudo make' cpan> o conf mbuild_install_build_command 'sudo ./Build' cpan> o conf commit cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz .... and keep an eye on it... it will ask for a password early on to allow it to install into the right directories. Or you if you want to retry your current method you could do this sudo perl ./Build.pl HTH adam On 30 Jul 2010, at 10:37, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > - ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > is not installed on this computer. > Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > is not installed on this computer. > Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > is not installed on this computer. > stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > is not installed on this computer. > Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > is not installed on this computer. > stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > There are some external packages and perl modules, listed above, which > stag uses. This only effects the functionality which is listed above: > the rest of stag will work fine, which includes nearly all of the > core functionality. > > Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > CMUNGALL/Data-Stag-0.11.tar.gz > make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > 3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > 1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > 6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > 5/5 skipped: various reasons > t/set-attrs..........ok > 3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > 7/7 skipped: various reasons > t/xml2...............ok > 4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) > CMUNGALL/Data-Stag-0.11.tar.gz > make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at -e line 1 > make: *** [pure_site_install] Error 13 > CMUNGALL/Data-Stag-0.11.tar.gz > make install -- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > - ERROR: You chose to install Data::Stag but it failed to install > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > * Optional prerequisite Spreadsheet::ParseExcel is not installed > (wanted for parsing Excel files, used by Bio::SeqIO::excel) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite Graph is not installed > (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > * Optional prerequisite SVG::Graph is not installed > (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > * Optional prerequisite SOAP::Lite is not installed > (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > * Optional prerequisite Bio::ASN1::EntrezGene is not installed > (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Convert::Binary::C is not installed > (wanted for strider functionality, used by Bio::SeqIO::strider) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite XML::Twig is not installed > (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > * Optional prerequisite Set::Scalar is not installed > (wanted for proper operation, used by Bio::Tree::Compatible) > * Optional prerequisite XML::Parser::PerlSAX is not installed > (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > * Optional prerequisite XML::SAX::Writer is not installed > (wanted for writing xml, used by Bio::SeqIO::tigrxml) > * Optional prerequisite Clone is not installed > (wanted for cloning objects, used by Bio::Tools::Primer3) > * Optional prerequisite XML::DOM::XPath is not installed > (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > * Optional prerequisite PostScript::TextBlock is not installed > (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > BioDBGFF.................disabled > * MySQL, Pg nor Oracle DBI drivers are installed > BioDBSeqFeature_mysql....disabled > - DBD::mysql is not installed > Network..................enabled > BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > - will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > - will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # Failed test 'use Bio::Annotation::TagTree;' > # at t/Annotation/Annotation.t line 20. > # Tried to use 'Bio::Annotation::TagTree'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # Failed test 'default itext' > # at t/Annotation/Annotation.t line 307. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > > # Failed test 'itext' > # at t/Annotation/Annotation.t line 315. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > 1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > 8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > Failed 17/19 tests, 10.53% okay > 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 > 11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > 9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > 19/267 skipped: various reasons > 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 > 10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > 10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > 4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > 14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > 13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > 10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > 10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > 8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > 3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > 2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > all 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.............................ok 1/1093 > # Failed (TODO) test at t/SearchIO/blast.t line 527. > # '0.852' > # > > # '0.9' > > # Failed (TODO) test at t/SearchIO/blast.t line 528. > # '1.599' > # <= > # '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # got: '0.946' > # expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # got: undef > # expected: '31984247' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # got: undef > # expected: '88780' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # got: undef > # expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > 4/45 skipped: various reasons > 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...........................ok 1/116 > # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # expected: undef > > # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # got: '\-\.=~' > # expected: '-\?' > > # Failed (TODO) test at t/Seq/LocatableSeq.t 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 > all 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 > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > 7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > all 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..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # Failed test 'use Bio::SeqIO::chaos;' > # at t/SeqIO/chaos.t line 15. > # Tried to use 'Bio::SeqIO::chaos'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > all 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 > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # Failed (TODO) test 'primary_id' > # at t/SeqIO/gcg.t line 54. > # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > all 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 > all 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 > all 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..................................ok 1/59 > # Failed (TODO) test 'accuracies' > # at t/SeqIO/scf.t line 78. > # got: 'ARRAY(0x100ac5648)' > # expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # Failed test 'use Bio::SeqIO::swiss;' > # at t/SeqIO/swiss.t line 12. > # Tried to use 'Bio::SeqIO::swiss'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > 112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # at t/SeqTools/GuessSeqFormat.t line 71. > # got: '0' > # expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > 5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > all 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 > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > 12/16 skipped: various reasons > 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 > all 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......................skipped > all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > 12/45 skipped: various reasons > 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 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 > all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > 2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > 3/4 skipped: various reasons > 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 > 15/26 skipped: various reasons > Failed Test Stat Wstat Total Fail List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t 255 65280 28 42 8-28 > t/AlignIO/arp.t 255 65280 48 92 3-48 > t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 > t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 > t/LocalDB/Flat.t 255 65280 24 20 15-24 > t/LocalDB/Index.t 255 65280 64 66 32-64 > t/SeqIO/Handler.t 255 65280 550 1098 2-550 > t/SeqIO/chaos.t 1 256 8 1 1 > t/SeqIO/swiss.t 255 65280 240 479 1-240 > t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 > t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From wkretzsch at gmail.com Fri Jul 30 11:37:08 2010 From: wkretzsch at gmail.com (Warren W. Kretzschmar) Date: Fri, 30 Jul 2010 11:37:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Alternatively I think you might have run "make install" when what you actually wanted to run was "sudo make install". The sudo means you install everything with root rights (which you say you have). It'll ask you for a password and then it will have the rights to install into /usr/local/bin Cheers, Warren On Fri, Jul 30, 2010 at 9:54 AM, Robson de Souza wrote: > Did you try, as root, > > ./Build.pl --install_base /opt/local > > ? > > Also, check the INSTALL file at the root of the bioperl distribution. > Robson > > On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: >> Hi there >> I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. >> I am not able to complete the installation as every time I get: >> >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> ?I have tried using both methods to install into a local folder and get the same thing >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/home/users/carrieomalley/bin' >> mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. >> >> >> If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( >> >> >> Many thanks in advance >> Carrie >> >> >> >> >> >> Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL >> Checking whether your kit is complete... >> Looks good >> >> Checking prerequisites... >> ?- ERROR: Data::Stag is not installed >> (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) >> CPAN: Storable loaded ok (v2.18) >> Going to read /Users/carrieomalley/.cpan/Metadata >> ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT >> Running install for module 'Data::Stag' >> 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' >> Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok >> x Data-Stag-0.11/ >> x Data-Stag-0.11/c-ext/ >> x Data-Stag-0.11/c-ext/README.c-ext >> x Data-Stag-0.11/c-ext/staglib.c >> x Data-Stag-0.11/c-ext/staglib.h >> x Data-Stag-0.11/Changes >> x Data-Stag-0.11/Data/ >> x Data-Stag-0.11/Data/Stag/ >> x Data-Stag-0.11/Data/Stag/Arr2HTML.pm >> x Data-Stag-0.11/Data/Stag/Base.pm >> x Data-Stag-0.11/Data/Stag/BaseGenerator.pm >> x Data-Stag-0.11/Data/Stag/BaseHandler.pm >> x Data-Stag-0.11/Data/Stag/ChainHandler.pm >> x Data-Stag-0.11/Data/Stag/DTDWriter.pm >> x Data-Stag-0.11/Data/Stag/GraphHandler.pm >> x Data-Stag-0.11/Data/Stag/HashDB.pm >> x Data-Stag-0.11/Data/Stag/IndentParser.pm >> x Data-Stag-0.11/Data/Stag/IndentWriter.pm >> x Data-Stag-0.11/Data/Stag/ITextParser.pm >> x Data-Stag-0.11/Data/Stag/ITextWriter.pm >> x Data-Stag-0.11/Data/Stag/null.pm >> x Data-Stag-0.11/Data/Stag/PerlWriter.pm >> x Data-Stag-0.11/Data/Stag/PodParser.pm >> x Data-Stag-0.11/Data/Stag/SAX2Stag.pm >> x Data-Stag-0.11/Data/Stag/Simple.pm >> x Data-Stag-0.11/Data/Stag/StagDB.pm >> x Data-Stag-0.11/Data/Stag/StagI.pm >> x Data-Stag-0.11/Data/Stag/StagImpl.pm >> x Data-Stag-0.11/Data/Stag/SxprParser.pm >> x Data-Stag-0.11/Data/Stag/SxprWriter.pm >> x Data-Stag-0.11/Data/Stag/Util.pm >> x Data-Stag-0.11/Data/Stag/Writer.pm >> x Data-Stag-0.11/Data/Stag/XMLParser.pm >> x Data-Stag-0.11/Data/Stag/XMLWriter.pm >> x Data-Stag-0.11/Data/Stag/XSLHandler.pm >> x Data-Stag-0.11/Data/Stag/XSLTHandler.pm >> x Data-Stag-0.11/Data/Stag.pm >> x Data-Stag-0.11/dev/ >> x Data-Stag-0.11/dev/create-manifest.sh >> x Data-Stag-0.11/dev/data-stag.spec >> x Data-Stag-0.11/dev/mkspec.pl >> x Data-Stag-0.11/elisp/ >> x Data-Stag-0.11/elisp/itext-mode.el >> x Data-Stag-0.11/homepage/ >> x Data-Stag-0.11/homepage/archBIG.png >> x Data-Stag-0.11/homepage/dbstag-tutorial.sgml >> x Data-Stag-0.11/homepage/images/ >> x Data-Stag-0.11/homepage/images/k-schema-diagram.png >> x Data-Stag-0.11/homepage/images/rr-schema-diagram.png >> x Data-Stag-0.11/homepage/index.html >> x Data-Stag-0.11/homepage/makefile >> x Data-Stag-0.11/homepage/mk.sh >> x Data-Stag-0.11/homepage/mkpodhtml.pl >> x Data-Stag-0.11/homepage/mkscriptdoc.pl >> x Data-Stag-0.11/homepage/script-docs/ >> x Data-Stag-0.11/homepage/script-docs/selectall_html.html >> x Data-Stag-0.11/homepage/script-docs/selectall_xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html >> x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html >> x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html >> x Data-Stag-0.11/homepage/script-docs/stag-db.html >> x Data-Stag-0.11/homepage/script-docs/stag-diff.html >> x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-elcount.html >> x Data-Stag-0.11/homepage/script-docs/stag-eval.html >> x Data-Stag-0.11/homepage/script-docs/stag-filter.html >> x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-flatten.html >> x Data-Stag-0.11/homepage/script-docs/stag-grep.html >> x Data-Stag-0.11/homepage/script-docs/stag-handle.html >> x Data-Stag-0.11/homepage/script-docs/stag-ir.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-join.html >> x Data-Stag-0.11/homepage/script-docs/stag-merge.html >> x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html >> x Data-Stag-0.11/homepage/script-docs/stag-parse.html >> x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html >> x Data-Stag-0.11/homepage/script-docs/stag-query.html >> x Data-Stag-0.11/homepage/script-docs/stag-show-template.html >> x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html >> x Data-Stag-0.11/homepage/script-docs/stag-splitter.html >> x Data-Stag-0.11/homepage/script-docs/stag-storenode.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html >> x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html >> x Data-Stag-0.11/homepage/script-docs/stag-view.html >> x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html >> x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html >> x Data-Stag-0.11/homepage/script-list.html >> x Data-Stag-0.11/homepage/stag-db-tutorial.html >> x Data-Stag-0.11/homepage/stag-poster.html >> x Data-Stag-0.11/INSTALL >> x Data-Stag-0.11/Makefile.PL >> x Data-Stag-0.11/MANIFEST >> x Data-Stag-0.11/META.yml >> x Data-Stag-0.11/README >> x Data-Stag-0.11/scripts/ >> x Data-Stag-0.11/scripts/stag-autoschema.pl >> x Data-Stag-0.11/scripts/stag-db.pl >> x Data-Stag-0.11/scripts/stag-diff.pl >> x Data-Stag-0.11/scripts/stag-drawtree.pl >> x Data-Stag-0.11/scripts/stag-elcount.pl >> x Data-Stag-0.11/scripts/stag-eval.pl >> x Data-Stag-0.11/scripts/stag-filter.pl >> x Data-Stag-0.11/scripts/stag-findsubtree.pl >> x Data-Stag-0.11/scripts/stag-flatten.pl >> x Data-Stag-0.11/scripts/stag-grep.pl >> x Data-Stag-0.11/scripts/stag-handle.pl >> x Data-Stag-0.11/scripts/stag-itext2simple.pl >> x Data-Stag-0.11/scripts/stag-itext2sxpr.pl >> x Data-Stag-0.11/scripts/stag-itext2xml.pl >> x Data-Stag-0.11/scripts/stag-join.pl >> x Data-Stag-0.11/scripts/stag-merge.pl >> x Data-Stag-0.11/scripts/stag-mogrify.pl >> x Data-Stag-0.11/scripts/stag-parse.pl >> x Data-Stag-0.11/scripts/stag-query.pl >> x Data-Stag-0.11/scripts/stag-splitter.pl >> x Data-Stag-0.11/scripts/stag-view.pl >> x Data-Stag-0.11/scripts/stag-xml2itext.pl >> x Data-Stag-0.11/scripts/stag-xmlsplit.pl >> x Data-Stag-0.11/t/ >> x Data-Stag-0.11/t/animal.x >> x Data-Stag-0.11/t/autoschema.t >> x Data-Stag-0.11/t/barfly.x >> x Data-Stag-0.11/t/bio.x >> x Data-Stag-0.11/t/chainhandler.t >> x Data-Stag-0.11/t/collapse.x >> x Data-Stag-0.11/t/data/ >> x Data-Stag-0.11/t/data/attrs.xml >> x Data-Stag-0.11/t/data/bf.txt >> x Data-Stag-0.11/t/data/eco.el >> x Data-Stag-0.11/t/data/eco.itext >> x Data-Stag-0.11/t/data/homol.itext >> x Data-Stag-0.11/t/data/persons.el >> x Data-Stag-0.11/t/db.t >> x Data-Stag-0.11/t/emptytag.t >> x Data-Stag-0.11/t/get.t >> x Data-Stag-0.11/t/graph.x >> x Data-Stag-0.11/t/handlers.t >> x Data-Stag-0.11/t/handlers2.t >> x Data-Stag-0.11/t/handlers2.x >> x Data-Stag-0.11/t/hashdb.t >> x Data-Stag-0.11/t/hashdb.x >> x Data-Stag-0.11/t/homol.t >> x Data-Stag-0.11/t/lisp.x >> x Data-Stag-0.11/t/parsestr.t >> x Data-Stag-0.11/t/path.x >> x Data-Stag-0.11/t/path2.x >> x Data-Stag-0.11/t/qmatch.t >> x Data-Stag-0.11/t/roundtrip-attrs.t >> x Data-Stag-0.11/t/set-attrs.t >> x Data-Stag-0.11/t/set.t >> x Data-Stag-0.11/t/sxpr.t >> x Data-Stag-0.11/t/unhash.t >> x Data-Stag-0.11/t/unset.t >> x Data-Stag-0.11/t/write.t >> x Data-Stag-0.11/t/xml1.t >> x Data-Stag-0.11/t/xml2.t >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> >> >> External Module XML::LibXSLT, XSLT, >> ?is not installed on this computer. >> ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations >> >> External Module XML::Parser::PerlSAX, SAX Handler, >> ?is not installed on this computer. >> ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML >> >> External Module GD, Graphical Drawing Toolkit, >> ?is not installed on this computer. >> ?stag-drawtree.pl in Data::Stag needs it for drawing trees >> >> External Module Graph::Directed, Generic Graph data stucture and algorithms, >> ?is not installed on this computer. >> ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs >> >> External Module Tk, Tk, >> ?is not installed on this computer. >> ?stag-view.pl in Data::Stag needs it for tree viewer >> >> >> Information: >> >> ? There are some external packages and perl modules, listed above, which >> ? stag uses. This only effects the functionality which is listed above: >> ? the rest of stag will work fine, which includes nearly all of the >> ? core functionality. >> >> ? Enjoy the rest of stag, which you can use after going 'make install' >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Data >> Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites >> cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm >> cp Data/Stag.pm blib/lib/Data/Stag.pm >> cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm >> cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm >> cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm >> cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm >> cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm >> cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm >> cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm >> cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm >> cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm >> cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm >> cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm >> cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm >> cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm >> cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm >> cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm >> cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm >> cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm >> cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm >> cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm >> cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm >> cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm >> cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm >> cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm >> cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm >> cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm >> cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm >> cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm >> cp scripts/stag-view.pl blib/script/stag-view.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl >> cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl >> cp scripts/stag-grep.pl blib/script/stag-grep.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl >> cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl >> cp scripts/stag-merge.pl blib/script/stag-merge.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl >> cp scripts/stag-parse.pl blib/script/stag-parse.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl >> cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl >> cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl >> cp scripts/stag-join.pl blib/script/stag-join.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl >> cp scripts/stag-db.pl blib/script/stag-db.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl >> cp scripts/stag-filter.pl blib/script/stag-filter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl >> cp scripts/stag-handle.pl blib/script/stag-handle.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl >> cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl >> cp scripts/stag-query.pl blib/script/stag-query.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl >> cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl >> cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl >> cp scripts/stag-flatten.pl blib/script/stag-flatten.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl >> cp scripts/stag-splitter.pl blib/script/stag-splitter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl >> cp scripts/stag-diff.pl blib/script/stag-diff.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl >> cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl >> Manifying blib/man1/stag-view.pl.1 >> Manifying blib/man1/stag-mogrify.pl.1 >> Manifying blib/man1/stag-grep.pl.1 >> Manifying blib/man1/stag-handle.pl.1 >> Manifying blib/man1/stag-drawtree.pl.1 >> Manifying blib/man1/stag-query.pl.1 >> Manifying blib/man1/stag-merge.pl.1 >> Manifying blib/man1/stag-parse.pl.1 >> Manifying blib/man1/stag-findsubtree.pl.1 >> Manifying blib/man1/stag-join.pl.1 >> Manifying blib/man1/stag-autoschema.pl.1 >> Manifying blib/man1/stag-db.pl.1 >> Manifying blib/man1/stag-flatten.pl.1 >> Manifying blib/man1/stag-splitter.pl.1 >> Manifying blib/man1/stag-diff.pl.1 >> Manifying blib/man1/stag-filter.pl.1 >> Manifying blib/man3/Data::Stag::StagDB.3pm >> Manifying blib/man3/Data::Stag::SxprWriter.3pm >> Manifying blib/man3/Data::Stag.3pm >> Manifying blib/man3/Data::Stag::ChainHandler.3pm >> Manifying blib/man3/Data::Stag::IndentParser.3pm >> Manifying blib/man3/Data::Stag::Simple.3pm >> Manifying blib/man3/Data::Stag::SAX2Stag.3pm >> Manifying blib/man3/Data::Stag::Arr2HTML.3pm >> Manifying blib/man3/Data::Stag::XSLHandler.3pm >> Manifying blib/man3/Data::Stag::PerlWriter.3pm >> Manifying blib/man3/Data::Stag::XSLTHandler.3pm >> Manifying blib/man3/Data::Stag::DTDWriter.3pm >> Manifying blib/man3/Data::Stag::Writer.3pm >> Manifying blib/man3/Data::Stag::XMLWriter.3pm >> Manifying blib/man3/Data::Stag::GraphHandler.3pm >> Manifying blib/man3/Data::Stag::XMLParser.3pm >> Manifying blib/man3/Data::Stag::StagImpl.3pm >> Manifying blib/man3/Data::Stag::PodParser.3pm >> Manifying blib/man3/Data::Stag::BaseGenerator.3pm >> Manifying blib/man3/Data::Stag::IndentWriter.3pm >> Manifying blib/man3/Data::Stag::HashDB.3pm >> Manifying blib/man3/Data::Stag::null.3pm >> Manifying blib/man3/Data::Stag::ITextParser.3pm >> Manifying blib/man3/Data::Stag::BaseHandler.3pm >> Manifying blib/man3/Data::Stag::ITextWriter.3pm >> Manifying blib/man3/Data::Stag::SxprParser.3pm >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/autoschema.........ok >> t/chainhandler.......ok >> t/db.................ok >> t/emptytag...........ok >> ? ? ? ?3/3 skipped: various reasons >> t/get................ok >> t/handlers...........ok >> t/handlers2..........ok >> ? ? ? ?1/9 skipped: various reasons >> t/hashdb.............ok >> t/homol..............ok >> t/parsestr...........ok >> ? ? ? ?6/6 skipped: various reasons >> t/qmatch.............ok >> t/roundtrip-attrs....ok >> ? ? ? ?5/5 skipped: various reasons >> t/set-attrs..........ok >> ? ? ? ?3/3 skipped: various reasons >> t/set................ok >> t/sxpr...............ok >> t/unhash.............ok >> t/unset..............ok >> t/write..............ok >> t/xml1...............ok >> ? ? ? ?7/7 skipped: various reasons >> t/xml2...............ok >> ? ? ? ?4/4 skipped: various reasons >> All tests successful, 29 subtests skipped. >> Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make test -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make install >> Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at -e line 1 >> make: *** [pure_site_install] Error 13 >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make install ?-- NOT OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> >> *** (back in Bioperl Build.PL) *** >> Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n >> ?- ERROR: You chose to install Data::Stag but it failed to install >> ?* Optional prerequisite Ace is not installed >> ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) >> ?* Optional prerequisite Spreadsheet::ParseExcel is not installed >> ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) >> ?* Optional prerequisite Math::Random is not installed >> ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) >> ?* Optional prerequisite Graph is not installed >> ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) >> ?* Optional prerequisite SVG::Graph is not installed >> ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) >> ?* Optional prerequisite SOAP::Lite is not installed >> ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) >> ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed >> ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) >> ?* Optional prerequisite GraphViz is not installed >> ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) >> ?* Optional prerequisite Array::Compare is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite Convert::Binary::C is not installed >> ? (wanted for strider functionality, used by Bio::SeqIO::strider) >> ?* Optional prerequisite Algorithm::Munkres is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite XML::Twig is not installed >> ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) >> ?* Optional prerequisite Set::Scalar is not installed >> ? (wanted for proper operation, used by Bio::Tree::Compatible) >> ?* Optional prerequisite XML::Parser::PerlSAX is not installed >> ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) >> ?* Optional prerequisite XML::SAX::Writer is not installed >> ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) >> ?* Optional prerequisite Clone is not installed >> ? (wanted for cloning objects, used by Bio::Tools::Primer3) >> ?* Optional prerequisite XML::DOM::XPath is not installed >> ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) >> ?* Optional prerequisite PostScript::TextBlock is not installed >> ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions >> of the modules indicated above before proceeding with this installation >> >> Checking features: >> ?BioDBGFF.................disabled >> ? ?* MySQL, Pg nor Oracle DBI drivers are installed >> ?BioDBSeqFeature_mysql....disabled >> ? ?- DBD::mysql is not installed >> ?Network..................enabled >> ?BioDBSeqFeature_BDB......enabled >> >> Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] >> ?- will install all scripts >> >> Do you want to run tests that require connection to servers across the internet >> (likely to cause some failures)? y/n [n] n >> ?- will not run internet-requiring tests >> Deleting Build >> Removed previous script 'Build' >> >> Creating new 'Build' script for 'BioPerl' version '1.006000' >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> t/Align/AlignStats...........................ok >> t/Align/AlignUtil............................ok >> t/Align/SimpleAlign..........................ok >> t/Align/TreeBuild............................ok >> t/Align/Utilities............................ok >> t/AlignIO/AlignIO............................ok 1/28 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> # Looks like you planned 28 tests but only ran 7. >> # Looks like your test died just after 7. >> t/AlignIO/AlignIO............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 8-28 >> ? ? ? ?Failed 21/28 tests, 25.00% okay >> t/AlignIO/arp................................ok 1/48 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> # Looks like you planned 48 tests but only ran 2. >> # Looks like your test died just after 2. >> t/AlignIO/arp................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-48 >> ? ? ? ?Failed 46/48 tests, 4.17% okay >> 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......................ok 1/159 >> # ? Failed test 'use Bio::Annotation::TagTree;' >> # ? at t/Annotation/Annotation.t line 20. >> # ? ? Tried to use 'Bio::Annotation::TagTree'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. >> # Compilation failed in require at (eval 37) line 2. >> # BEGIN failed--compilation aborted at (eval 37) line 2. >> t/Annotation/Annotation......................NOK 9/159 >> # ? Failed test 'default itext' >> # ? at t/Annotation/Annotation.t line 307. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> >> # ? Failed test 'itext' >> # ? at t/Annotation/Annotation.t line 315. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. >> # Looks like you planned 159 tests but only ran 119. >> # Looks like you failed 3 tests of 119 run. >> # Looks like your test died just after 119. >> t/Annotation/Annotation......................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 9, 117, 119-159 >> ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) >> t/Annotation/AnnotationAdaptor...............ok >> t/Assembly/Assembly..........................ok 1/51 >> # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. >> t/Assembly/Assembly..........................ok >> t/Assembly/ContigSpectrum....................ok >> t/Biblio/Biblio..............................ok >> ? ? ? ?1/24 skipped: various reasons >> t/Biblio/References..........................ok >> t/Biblio/biofetch............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Biblio/eutils..............................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/ClusterIO/ClusterIO........................ok >> ? ? ? ?8/12 skipped: various reasons >> t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/ClusterIO/SequenceFamily.t:16 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. >> # Looks like you planned 19 tests but only ran 2. >> # Looks like your test died just after 2. >> t/ClusterIO/SequenceFamily...................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-19 >> ? ? ? ?Failed 17/19 tests, 10.53% okay >> 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 >> ? ? ? ?11/279 skipped: various reasons >> t/LocalDB/BlastIndex.........................ok >> t/LocalDB/DBFasta............................ok >> t/LocalDB/DBQual.............................ok >> t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 >> STACK: t/LocalDB/Flat.t:89 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. >> # Looks like you planned 24 tests but only ran 14. >> # Looks like your test died just after 14. >> t/LocalDB/Flat...............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-24 >> ? ? ? ?Failed 10/24 tests, 58.33% okay >> t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 >> STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 >> STACK: t/LocalDB/Index.t:91 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. >> # Looks like you planned 64 tests but only ran 31. >> # Looks like your test died just after 31. >> t/LocalDB/Index..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 32-64 >> ? ? ? ?Failed 33/64 tests, 48.44% okay >> t/LocalDB/Registry...........................ok >> ? ? ? ?9/14 skipped: various reasons >> t/LocalDB/SeqFeature.........................ok >> t/LocalDB/transfac_pro.......................ok >> t/Map/Cyto...................................ok >> t/Map/Linkage................................ok >> t/Map/Map....................................ok >> ? ? ? ?19/267 skipped: various reasons >> 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 >> ? ? ? ?10/14 skipped: various reasons >> t/Matrix/SiteMatrix..........................ok >> t/Ontology/GOterm............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/GraphAdaptor......................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/go.............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/interpro.......................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/Ontology/IO/obo............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Ontology..........................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/OntologyEngine....................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/OntologyStore.....................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Relationship......................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/RelationshipType..................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/Term..............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Perl.......................................ok >> ? ? ? ?10/29 skipped: various reasons >> 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..................................ok >> t/PopGen/Coalescent..........................ok >> t/PopGen/HtSNP...............................ok >> t/PopGen/MK..................................ok >> ? ? ? ?4/46 skipped: various reasons >> t/PopGen/PopGen..............................ok >> t/PopGen/PopGenSims..........................ok >> t/PopGen/TagHaplotype........................ok >> t/RemoteDB/BioFetch..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/CUTG..............................ok >> ? ? ? ?14/37 skipped: various reasons >> t/RemoteDB/DB................................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EMBL..............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EUtilities........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/HIV/HIV...........................ok >> ? ? ? ?13/30 skipped: various reasons >> t/RemoteDB/HIV/HIVAnnotProcessor.............ok >> t/RemoteDB/HIV/HIVQuery......................ok >> ? ? ? ?10/41 skipped: various reasons >> t/RemoteDB/HIV/HIVQueryHelper................ok >> t/RemoteDB/RefSeq............................ok >> ? ? ? ?10/16 skipped: various reasons >> t/RemoteDB/SeqHound..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqRead_fail......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqVersion........................ok >> ? ? ? ?8/10 skipped: various reasons >> t/RemoteDB/Taxonomy..........................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/Restriction/Analysis.......................ok >> t/Restriction/Gel............................ok >> t/Restriction/IO.............................ok 1/18 >> # ? Failed (TODO) test at t/Restriction/IO.t line 31. >> t/Restriction/IO.............................ok >> ? ? ? ?3/18 skipped: various reasons >> t/Root/Exception.............................ok >> t/Root/RootI.................................ok >> t/Root/RootIO................................ok >> ? ? ? ?2/31 skipped: various reasons >> t/Root/Storable..............................ok >> t/Root/Tempfile..............................ok >> t/Root/Utilities.............................ok >> t/SearchDist.................................skipped >> ? ? ? ?all 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.............................ok 1/1093 >> # ? Failed (TODO) test at t/SearchIO/blast.t line 527. >> # ? ? '0.852' >> # ? ? ? ? > >> # ? ? '0.9' >> >> # ? Failed (TODO) test at t/SearchIO/blast.t line 528. >> # ? ? '1.599' >> # ? ? ? ? <= >> # ? ? '1' >> t/SearchIO/blast.............................ok >> t/SearchIO/blast_pull........................ok 1/289 >> # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. >> # ? ? ? ? ?got: '0.946' >> # ? ? expected: '0.943' >> t/SearchIO/blast_pull........................ok >> t/SearchIO/blasttable........................ok >> t/SearchIO/blastxml..........................ok 1/298 >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. >> # ? ? ? ? ?got: undef >> # ? ? expected: '31984247' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. >> # ? ? ? ? ?got: undef >> # ? ? expected: '88780' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. >> # ? ? ? ? ?got: undef >> # ? ? expected: '49' >> t/SearchIO/blastxml..........................ok >> t/SearchIO/cross_match.......................ok >> t/SearchIO/erpin.............................ok >> t/SearchIO/exonerate.........................ok >> ? ? ? ?4/45 skipped: various reasons >> 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...........................ok 1/116 >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. >> # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' >> # ? ? expected: undef >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. >> # ? ? ? ? ?got: '\-\.=~' >> # ? ? expected: '-\?' >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature......................ok >> ? ? ? ?7/214 skipped: various reasons >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> t/SeqIO......................................ok >> t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. >> BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqIO/Handler.t:20 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. >> # Looks like you planned 550 tests but only ran 1. >> # Looks like your test died just after 1. >> t/SeqIO/Handler..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 2-550 >> ? ? ? ?Failed 549/550 tests, 0.18% okay >> t/SeqIO/MultiFile............................ok >> t/SeqIO/Multiple_fasta.......................ok >> t/SeqIO/SeqBuilder...........................ok >> t/SeqIO/Splicedseq...........................ok >> t/SeqIO/abi..................................skipped >> ? ? ? ?all 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..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/asciitree............................ok >> t/SeqIO/bsml.................................skipped >> ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed >> t/SeqIO/bsml_sax.............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/chadoxml.............................ok >> t/SeqIO/chaos................................ >> # ? Failed test 'use Bio::SeqIO::chaos;' >> # ? at t/SeqIO/chaos.t line 15. >> # ? ? Tried to use 'Bio::SeqIO::chaos'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. >> # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> # Looks like you failed 1 test of 8. >> t/SeqIO/chaos................................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED test 1 >> ? ? ? ?Failed 1/8 tests, 87.50% okay >> t/SeqIO/chaosxml.............................skipped >> ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed >> t/SeqIO/ctf..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/embl.................................ok >> t/SeqIO/entrezgene...........................skipped >> ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed >> t/SeqIO/excel................................skipped >> ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed >> t/SeqIO/exp..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/gcg..................................ok 1/17 >> # ? Failed (TODO) test 'primary_id' >> # ? at t/SeqIO/gcg.t line 54. >> # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' >> # ? ? expected: 'roa1_drome' >> t/SeqIO/gcg..................................ok >> t/SeqIO/genbank..............................ok >> t/SeqIO/interpro.............................skipped >> ? ? ? ?all 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 >> ? ? ? ?all 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 >> ? ? ? ?all 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..................................ok 1/59 >> # ? Failed (TODO) test 'accuracies' >> # ? at t/SeqIO/scf.t line 78. >> # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' >> # ? ? expected: '482' >> t/SeqIO/scf..................................ok >> t/SeqIO/strider..............................skipped >> ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed >> t/SeqIO/swiss................................ >> # ? Failed test 'use Bio::SeqIO::swiss;' >> # ? at t/SeqIO/swiss.t line 12. >> # ? ? Tried to use 'Bio::SeqIO::swiss'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. >> # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. >> # Looks like you planned 240 tests but only ran 1. >> # Looks like you failed 1 test of 1 run. >> # Looks like your test died just after 1. >> t/SeqIO/swiss................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-240 >> ? ? ? ?Failed 240/240 tests, 0.00% okay >> t/SeqIO/tab..................................ok >> t/SeqIO/table................................ok >> ? ? ? ?112/450 skipped: various reasons >> t/SeqIO/tigr.................................ok >> t/SeqIO/tigrxml..............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/tinyseq..............................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/ztr..................................skipped >> ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqTools/GuessSeqFormat.t:62 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> t/SeqTools/GuessSeqFormat....................NOK 25/49 >> # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. >> # ' >> # ? at t/SeqTools/GuessSeqFormat.t line 71. >> # ? ? ? ? ?got: '0' >> # ? ? expected: '1' >> # Looks like you planned 49 tests but ran 1 extra. >> # Looks like you failed 1 test of 50 run. >> t/SeqTools/GuessSeqFormat....................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED tests 25, 50 >> ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) >> t/SeqTools/OddCodes..........................ok >> t/SeqTools/SeqPattern........................ok >> t/SeqTools/SeqStats..........................ok >> t/SeqTools/SeqUtils..........................ok >> t/SeqTools/SeqWords..........................ok >> t/Species....................................ok >> ? ? ? ?5/21 skipped: various reasons >> t/Structure/IO...............................ok >> t/Structure/Structure........................ok >> t/Symbol.....................................ok >> t/TaxonTree..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Domcut..............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/ELM.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/GOR4................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/HNN.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Mitoprot............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/NetPhos.............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/Tools/Analysis/Protein/Scansite.t:23 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. >> # Looks like you planned 14 tests but only ran 4. >> # Looks like your test died just after 4. >> t/Tools/Analysis/Protein/Scansite............dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 5-14 >> ? ? ? ?Failed 10/14 tests, 28.57% okay >> t/Tools/Analysis/Protein/Sopma...............ok >> ? ? ? ?12/16 skipped: various reasons >> 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 >> ? ? ? ?all 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......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Run/StandAloneBlast..................ok >> ? ? ? ?12/45 skipped: various reasons >> 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 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 >> ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed >> t/Tree/Node..................................ok >> t/Tree/PhyloNetwork/Factory..................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/GraphViz.................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/MuVector.................ok >> t/Tree/PhyloNetwork/PhyloNetwork.............skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/RandomFactory............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/TreeFactory..............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/RandomTreeFactory.....................ok >> t/Tree/Tree..................................ok >> t/Tree/TreeIO................................ok >> ? ? ? ?2/74 skipped: various reasons >> t/Tree/TreeIO/lintree........................ok >> t/Tree/TreeIO/newick.........................ok >> t/Tree/TreeIO/nexus..........................ok >> t/Tree/TreeIO/nhx............................ok >> t/Tree/TreeIO/phyloxml.......................ok >> t/Tree/TreeIO/svggraph.......................ok >> ? ? ? ?3/4 skipped: various reasons >> 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 >> ? ? ? ?15/26 skipped: various reasons >> Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed >> ------------------------------------------------------------------------------- >> t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 >> t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 >> t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 >> t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 >> t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 >> t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 >> t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 >> t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 >> t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 >> t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 >> t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 >> 57 tests and 313 subtests skipped. >> Failed 11/318 test scripts. 970/17228 subtests failed. >> Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) >> Failed 11/318 test programs. 970/17228 subtests failed. >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 >> Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 >> Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 >> Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 >> Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 >> Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 >> Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 >> Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 >> Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 >> Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 >> Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 >> Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 >> Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 >> Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 >> Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 >> Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 >> Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 >> Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 >> Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 >> Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 >> Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 >> Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 >> Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 >> Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 >> Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 >> Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 >> Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 >> Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 >> Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 >> Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 >> Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 >> Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 >> Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 >> Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 >> Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 >> Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 >> Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 >> Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 >> Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 >> Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 >> Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 >> Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 >> Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 >> Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 >> Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 >> Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 >> Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 >> Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 >> Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 >> Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 >> Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 >> Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 >> Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 >> Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 >> Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 >> Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 >> Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 sdshlxh at gmail.com Fri Jul 30 13:14:23 2010 From: sdshlxh at gmail.com (Ping Yao) Date: Fri, 30 Jul 2010 12:14:23 -0500 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: please remove me from the list. From Kevin.M.Brown at asu.edu Fri Jul 30 13:29:25 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Fri, 30 Jul 2010 10:29:25 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: <1A4207F8295607498283FE9E93B775B406D682E2@EX02.asurite.ad.asu.edu> You can remove yourself by following the link at the bottom of every email. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ping Yao Sent: Friday, July 30, 2010 10:14 AM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 please remove me from the list. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Sat Jul 31 16:56:49 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sat, 31 Jul 2010 16:56:49 -0400 Subject: [Bioperl-l] SOAP Eutilities Message-ID: Hi, Bio::DB::SoapEUtilities, referred in the HOWTO on EUtilities, seems to have disappeared from the Git repository. A simple git clone git://github.com/bioperl/bioperl-live.git does not download it. Any ideas why? Robson From twaddlac at gmail.com Thu Jul 1 14:45:01 2010 From: twaddlac at gmail.com (twaddlac) Date: Thu, 1 Jul 2010 07:45:01 -0700 (PDT) Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? Message-ID: <29046535.post@talk.nabble.com> Hi, I am having a bit of trouble reading in a qual file; I would like to input the qual file into a hash but I can't seem to find a method that returns the qual sequence. Any ideas? Thank you in advance! -- View this message in context: http://old.nabble.com/Read-in-a-Qual-File-like-a-Fasta--tp29046535p29046535.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From rmb32 at cornell.edu Fri Jul 2 00:18:58 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Thu, 01 Jul 2010 17:18:58 -0700 Subject: [Bioperl-l] Re ad in a Qual File like a Fasta? In-Reply-To: <29046535.post@talk.nabble.com> References: <29046535.post@talk.nabble.com> Message-ID: <4C2D3072.6080803@cornell.edu> You probably want to do something like: use Bio::SeqIO; my $qual_in = Bio::SeqIO->new( -format => 'qual', -file => $ARGV[0], ); while( my $q = $qual_in->next_seq ) { print "qual for ".$q->id." is: "; print "$_ " for @{ $q->qual }; print "\n"; } twaddlac wrote: > Hi, > > I am having a bit of trouble reading in a qual file; I would like to > input the qual file into a hash but I can't seem to find a method that > returns the qual sequence. Any ideas? Thank you in advance! From cjfields at illinois.edu Fri Jul 2 13:48:19 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 08:48:19 -0500 Subject: [Bioperl-l] BioPerl Switching to GitHub Organization Message-ID: <50D544D2-5F49-482F-9E7F-EB462871B380@illinois.edu> GitHub (as expected) just released their setup for organizations, including open-source projects. The announcement is here: http://github.com/blog/674-introducing-organizations I have already moved bioperl over to an organization account and have added a few co-owners of the github repository. The move is transparent, no one should notice any difference in checking out code. I'm working on reassigning teams to projects at this time, so please post here if there are any problems. chris From iatropoul at gmail.com Fri Jul 2 04:21:09 2010 From: iatropoul at gmail.com (George Iatropoulos) Date: Thu, 1 Jul 2010 21:21:09 -0700 (PDT) Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) Message-ID: Hi guys! I'd like to thank you for this important project. I currently develop a script that uses the SeqIO module to read fasta or files with other bio-formats. However your installation instructions are too difficult to be followed, or even outdated, especially for the mac platform. After trying a week I really can't install bioperl on a Snow Leopard machine (perl 5.10.0) and I tried the CPAN and the fink method. None of them works! Especially cpan seems to mess up with itself and now doesn't install anything! As for the ubuntu platform a simple command like: "sudo apt-get install bioperl" simply does the trick! However I couldn't find this simple command in your installation guidelines, and I don't really understand why I should set up a server, before installing bioperl and then follow this complicated series of instructions, to achieve something that is so simple! I understand that you try to give complete instructions for people who may be pleased with more advanced stuff, but please don't forget biology students who don't have a deep computational background. These guys like me would appreciate some simple stuff to get their job and their projects done, without needing to waste days to figure out complicated-guru stuff. Best wishes and many thanks to all of you because bioperl is really important for us! Georgios Iatropoulos From cjfields at illinois.edu Fri Jul 2 15:46:46 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jul 2010 10:46:46 -0500 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: References: Message-ID: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > Hi guys! > > I'd like to thank you for this important project. I currently develop > a script that uses the SeqIO module to read fasta or files with other > bio-formats. However your installation instructions are too difficult > to be followed, or even outdated, especially for the mac platform. > > After trying a week I really can't install bioperl on a Snow Leopard > machine (perl 5.10.0) and I tried the CPAN and the fink method. None > of them works! Especially cpan seems to mess up with itself and now > doesn't install anything! That's odd. Can you send me what you are seeing? > As for the ubuntu platform a simple command like: "sudo apt-get > install bioperl" simply does the trick! > However I couldn't find this simple command in your installation > guidelines, and I don't really understand why I should set up a > server, before installing bioperl and then follow this complicated > series of instructions, to achieve something that is so simple! That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > I understand that you try to give complete instructions for people who > may be pleased with more advanced stuff, but please don't forget > biology students who don't have a deep computational background. These > guys like me would appreciate some simple stuff to get their job and > their projects done, without needing to waste days to figure out > complicated-guru stuff. We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > Best wishes and many thanks to all of you because bioperl is really > important for us! > > Georgios Iatropoulos Sorry for the troubles, and thanks for letting us know. Any additional details about installation problems are very welcome. Also, the installation page on the bioperl website is editable (it is a wiki :). So, feel free to add more detail where needed, or use the discussion page to point out problems. chris From steffen_moeller at gmx.de Fri Jul 2 16:39:00 2010 From: steffen_moeller at gmx.de (=?ISO-8859-1?Q?Steffen_M=F6ller?=) Date: Fri, 02 Jul 2010 18:39:00 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <4C2E1624.2070402@gmx.de> Hello, On 07/02/2010 05:46 PM, Chris Fields wrote: > On Jul 1, 2010, at 11:21 PM, George Iatropoulos wrote: > > >> Hi guys! >> >> I'd like to thank you for this important project. I currently develop >> a script that uses the SeqIO module to read fasta or files with other >> bio-formats. However your installation instructions are too difficult >> to be followed, or even outdated, especially for the mac platform. >> >> After trying a week I really can't install bioperl on a Snow Leopard >> machine (perl 5.10.0) and I tried the CPAN and the fink method. None >> of them works! Especially cpan seems to mess up with itself and now >> doesn't install anything! >> > That's odd. Can you send me what you are seeing? > > >> As for the ubuntu platform a simple command like: "sudo apt-get >> install bioperl" simply does the trick! >> However I couldn't find this simple command in your installation >> guidelines, and I don't really understand why I should set up a >> server, before installing bioperl and then follow this complicated >> series of instructions, to achieve something that is so simple! >> > That's b/c the bioperl that is installed with apt is not up to date. CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for bioperl-run (where CPAN is at v.1.6.1). > this depends on the age of your distribution rather than on what is apt-get-able from various places. Debian Squeeze has 1.6.1, and so does Ubuntu since Lucid. http://packages.qa.debian.org/b/bioperl.html https://launchpad.net/ubuntu/+source/bioperl > I would like to get the releases to a point where they are easily packaged for apt/yum/ppm/fink/macports/whatever, so any help along those lines is greatly appreciated. Now, re: Ubuntu I haven't had any problems with 9.04 or 9.10 (haven't jumped into 10.04 yet), but I'm a core bioperl dev. There are a few recommended modules that require outside libraries (GD first among them). These modules are not required for most core functionality. > > I am CCing the Debian-Med list just in case they have some better idea here, but what I suggest if you don't want to >> I understand that you try to give complete instructions for people who >> may be pleased with more advanced stuff, but please don't forget >> biology students who don't have a deep computational background. These >> guys like me would appreciate some simple stuff to get their job and >> their projects done, without needing to waste days to figure out >> complicated-guru stuff. >> > We're actually working on segmenting BioPerl into separate packages, something I intend on bringing up next week at BOSC. > The intention of us Debian- and Ubuntu-Helpers is very much also to help you X-core guys to concentrate on whatever you want to concentrate on and by taking as many of the "cannot build this or that" questions away from you as we possibly can. From our point of view, karmic or lenny are already rather ancient. As a BioPerl developer you probably don't want to run any of the packages in your routine anyway, so there is not much of a point to update for you. But I share your concern for production sites that want to sync with your vibrant development. If one wants to stay with binaries I see apt-pinning and backports.org. If one would just add the Debian sources of unstable to the /etc/apt/sources.list, then one could also very easily create distribution-adjusted packages oneself by apt-get source -b bioperl, which would then execute "the make" for you. The original request for a pointer to the Debian/Ubuntu packages would be nice, indeed. We'll see us at BOSC next week. If there is anything you think we should do to help your experience with the distributions then please drop us a line or grep for me in Boston. The segmentation is no problem for the packaging, but possibly more so for the regular user with a biological background. Best, Steffen From kai.blin at biotech.uni-tuebingen.de Sat Jul 3 07:05:26 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Sat, 03 Jul 2010 09:05:26 +0200 Subject: [Bioperl-l] Installing Bioperl on Ubuntu and Mac OS X Snow Leopard (perl 5.10.0) In-Reply-To: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> References: <6E47FD9A-DB22-4997-8908-E9F65C1FAACA@illinois.edu> Message-ID: <1278140726.2833.77.camel@gonzo.home.kblin.org> On Fri, 2010-07-02 at 10:46 -0500, Chris Fields wrote: Hi Chris, > > As for the ubuntu platform a simple command like: "sudo apt-get > > install bioperl" simply does the trick! > > However I couldn't find this simple command in your installation > > guidelines, and I don't really understand why I should set up a > > server, before installing bioperl and then follow this complicated > > series of instructions, to achieve something that is so simple! > > That's b/c the bioperl that is installed with apt is not up to date. > CPAN has v.1.6.1; apt for karmic had 1.6.0 last I looked, v1.5.2 for > bioperl-run (where CPAN is at v.1.6.1). As Steffen already said, the current Ubuntu version is 1.6.1, for both bioperl and bioperl-run. I don't think providing backports for Debian/Ubuntu versions wouldn't be too hard. > I would like to get the releases to a point where they are easily > packaged for apt/yum/ppm/fink/macports/whatever, so any help along > those lines is greatly appreciated. There currently is only an "automated port" of Bioperl on the openSuse Build Service (OBS). I'll probably end up looking into packaging BioPerl for SLES11, and would do that on OBS. Supporting other suse distros is trivial, other RPM-based distros are doable once you figure out the package names. I'd say if Debian, Fedora, Suse and Ubuntu are covered, you're doing pretty fine for Linux. People using more exotic distros will be used to build their own stuff anyway. :) I've got no idea about packaging for OSX. > > I understand that you try to give complete instructions for people who > > may be pleased with more advanced stuff, but please don't forget > > biology students who don't have a deep computational background. These > > guys like me would appreciate some simple stuff to get their job and > > their projects done, without needing to waste days to figure out > > complicated-guru stuff. I think some of the instructions on installing BioPerl are pretty concise and allow you to just copy&paste the commands (see the ubuntu-server install instructions). They might be a bit outdated, I didn't check that. And of course I agree that it would be nicer if you could just point your package manager at the appropriate repository and be done. However, there's only a few people working on BioPerl, and packaging can eat a lot of time, as does keeping install instructions up-to-date. Especially on install instructions, every user can help. Once you wasted days on figuring out the complicated guru-stuff, write a wiki page to explain it in a less complicated way. :) Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From maizemu at gmail.com Sat Jul 3 15:30:14 2010 From: maizemu at gmail.com (Christopher Bottoms) Date: Sat, 3 Jul 2010 10:30:14 -0500 Subject: [Bioperl-l] Fwd: Codefest 2010: Final details In-Reply-To: References: <20100702133822.GA8735@sobchak.mgh.harvard.edu> Message-ID: I will be there first thing Wednesday morning. I'd be glad to help work on any project. On Sat, Jul 3, 2010 at 9:15 AM, Chris Fields wrote: > I will be there on the afternoon of the 7th. There are a couple of > projects one can look into for Moose and Perl 6 (Biome and BioPerl6). I > think Hilmar was to do some DBIx::Class stuff for BioSQL at one point, not > sure where that is (might be surplanted by SQLite work?). Would be nice to > talk with Mark re: the wrapper system for BioPerl as well. > > So lots of stuff to think over and plan for. Maybe we should move this to > open-bio-l, or bioperl-l? > > chris (fields) > > On Jul 3, 2010, at 12:44 AM, Heikki Lehvaslaiho wrote: > > > Chris, > > > > I do not have too much experience on cloud computing, either. There > > will be quite a few people from BioPerl . We'll meet and come up with > > a plan first thing in the morning. Unless someone has a very good one > > ready for sharing... > > > > -Heikki > > > > Heikki Lehvaslaiho - skype:heikki_lehvaslaiho > > cell: +966 545 595 849 office: +966 2 808 2429 > > > > Computational Bioscience Research Centre (CBRC), Building #2, Office > #4216 > > 4700 King Abdullah University of Science and Technology (KAUST) > > Thuwal 23955-6900, Kingdom of Saudi Arabia > > > > > > > > > > On 3 July 2010 08:36, Christopher Bottoms wrote: > >> Hi all, > >> > >> I was originally planning on working on cloud computing at the Codefest. > >> However, the 2-day cloud computing tutorial that I was going to attend > in > >> mid June was canceled. Does anyone have any programming that they would > like > >> help with? I have experience with Perl 5, including Moose, and I am > starting > >> to dabble in Perl 6. I have also programmed in Java in the past. I hear > >> Python is easy to learn, so I'd be open to working on a Python project > as > >> well. > >> > >> Thanks, > >> Christopher Bottoms > >> > >> On Fri, Jul 2, 2010 at 8:38 AM, Brad Chapman > wrote: > >>> > >>> Hi all; > >>> Codefest 2010 is finally here: next Wednesday and Thursday at > >>> Harvard Medical School and Massachusetts General Hospital in > >>> beautiful Boston. All of the logistics, directions and details > >>> are on the wiki page: > >>> > >>> http://www.open-bio.org/wiki/Codefest_2010 > >>> > >>> If you want the short version: show up at Harvard Medical School on > >>> Wednesday at 10am and we'll take care of the rest. Thanks to the > >>> hard work of Oliver, Kimberly, Leah, Toshiaki, and Mitsuteru we'll > >>> have coffee, lunches and internet. Thanks to Steffen and Ntino, > >>> we'll have Amazon credits to utilize. And of course, there will be > >>> BBQ and drinking on Thursday night when we are finished. > >>> > >>> I'm looking forward to a fun and productive time. The general plan > >>> will be to spend a bit of time on Wednesday morning organizing > >>> ourselves into like minded groups of folks, and then commence with > >>> coding and collaborating. > >>> > >>> If you aren't able to make it and you're listed on the wiki page under > >>> participants, please do cross your name off so we have a good idea of > >>> final numbers. Likewise, if you are coming but haven't put your name up > >>> there please add it. > >>> > >>> If you are interested in helping with making software and data > >>> available on shared cloud resources, here are the latest Amazon > >>> AMIs, snapshots, and the code base: > >>> > >>> Cloud BioLinux images: > >>> 64bit: ami-d62cc4bf > >>> 32bit: ami-5423cb3d > >>> > >>> An EBS public snapshot with indexed genomes: > >>> snap-67446d0f > >>> > >>> Infrastructure: > >>> http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/ > >>> > >>> Send an e-mail with any questions, thoughts or concerns. My phone > >>> number is 617-447-8586 in case you end up hopelessly lost somewhere > >>> in Boston and are desperate to begin programming. > >>> > >>> Looking forward to seeing everyone next Wednesday, > >>> Brad > >> > >> > > From cjfields at illinois.edu Sat Jul 3 18:23:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:23:08 -0500 Subject: [Bioperl-l] Error when Using BLAT???? In-Reply-To: References: Message-ID: <1D738754-1FA5-40CB-B805-27A3A36FF319@illinois.edu> On Jun 29, 2010, at 8:58 AM, Minh Bui wrote: > Hi everyone, > I am writing an application that allows me to search through a database > (yeast.nt*) *with a few queries (yeastquery.fasta). Here is the code: > > *use warnings;* > *use Bio::Tools::Run::Alignment::Blat;* > *use Bio::SeqIO;* > *use Bio::DB::Fasta;* > * * > *my $seqio_object = Bio::SeqIO -> new (-file => > 'C:/Users/MINH/Desktop/yeastquery.fasta', -format => 'fasta'); * > * * > *my $database = 'C:/Users/MINH/Desktop/yeast.nt';* > *my $db = Bio::DB::Fasta->new($database); * > * * > *my $factory = Bio::Tools::Run::Alignment::Blat->new(); * > * > * > *while (my $blat_object = $seqio_object -> next_seq) {** * > * my $results = $factory -> run($blat_object,$db); * > *}* > > > BUT i got this error and don't know how to fix it. I am sorry, i am new to > Perl and Bioperl. I am using window 7, Strawberry. > > > *Replacement list is longer than search list at > C:/strawberry/perl/site/lib/Bio/Range.pm line 251.* > *Use of uninitialized value in concatenation (.) or string at > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm line 251, > line 1.* The above are warnings from perl 5.12 that can be ignored (they have been fixed in bioperl-live on github). > *'-out' is not recognized as an internal or external command,* > *operable program or batch file.* > * > * > *------------- EXCEPTION: Bio::Root::Exception -------------* > *MSG: Blat call ( -out=psl C:\Users\MINH\AppData\Local\Temp\BUiXTGzYC2 > C:\Users\MINH\AppData\Local\Temp\yQK5pzgJ_z) crashed: 256 * > * > * > *STACK: Error::throw* > *STACK: Bio::Root::Root::throw > C:/strawberry/perl/site/lib/Bio/Root/Root.pm:368* > *STACK: Bio::Tools::Run::Alignment::Blat::_run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:261* > *STACK: Bio::Tools::Run::Alignment::Blat::run > C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:178* > *STACK: D:/eclipswp/bioperl/readfasta.pl:15* > *-----------------------------------------------------------* > > Thank you for your help. That may be a bug; I can check on it (I'm planning on setting up a BLAT pipeline here in the next few days). chris From cjfields at illinois.edu Sat Jul 3 18:27:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 13:27:32 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: No comments. I'm assuming this is okay to merge into master branch, so will merge in later today. chris On Jun 30, 2010, at 12:35 PM, Chris Fields wrote: > All, > > I have a branch in github (topic/species_proxy) that converts > Bio::Species into a proxy class. This appears to fix a ton of problems > introduced during the Tree/Taxonomy refactoring a few years back. > > Advantages: > > 1) No need for Scalar::Util::weaken within Bio::Species or > Bio::Tree::Node. Cleanup methods are handled during instance > destruction. > > 2) This paves the way a bit more for eventual deprecation of > Bio::Species in 1.7. > > 3) Works with bioperl-db and BioSQL as is (passes on both my local > Ubuntu 9.10 and Mac OS X 10.6), perl 5.10 and 5.12, should work with > earlier perl versions. > > Disadvantages: > > 1) For every Bio::Species, we have a Bio::Taxon, a Bio::Tree::Tree, and > a Bio::DB::Taxonomy (one instance more than the previous Bio::Species > implementation). We can probably reduce that down considerably by > creating the needed instances lazily. > > This fixes: > > bug 3017 use threads to get genbank file error > bug 2594 Bio::Species memory leak > > and possibly others: > > bug 2773 Bio::Tree::Node gets destroyed even though it is still live > > If there are no comments, I'll merge this with the master branch in the > next few days. > > ++++++++++++++++++++++++++++++++++++++++++ > > (NOTE: skip the next two paragraphs if you don't want to read nasty > implementation details) > > Bio::Species had previously inherited from Bio::Taxon, but also required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). > > The above proxy fix converts Bio::Species into a proxy class, which only > inherits the interface (Bio::Tree::NodeI), and delegates to an internal > Bio::Taxon and a Bio::Tree::Tree. Neither contained object has a > reference back to the Bio::Species instance, thus the class can perform > proper garbage collection. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at drycafe.net Sat Jul 3 20:55:30 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 3 Jul 2010 16:55:30 -0400 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> Message-ID: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > Bio::Species had previously inherited from Bio::Taxon, but also > required > it to hold a Bio::Tree::Tree which contained a circular reference back > to the Bio::Species object, thus requiring Scalar::Util::weaken. This > has caused several hard-to-diagnose problems with premature garbage > collection, including some issues with threads (bug 3017). Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sat Jul 3 23:36:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jul 2010 18:36:15 -0500 Subject: [Bioperl-l] Seeking comments, Bio::Species memleak fix In-Reply-To: <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> References: <1277919351.21543.66.camel@pyrimidine.igb.uiuc.edu> <8D0E35BF-3D55-4417-B738-282470AAB587@drycafe.net> Message-ID: <57B6FE86-FF5E-4579-B3FB-A2D7AB366117@illinois.edu> On Jul 3, 2010, at 3:55 PM, Hilmar Lapp wrote: > On Jun 30, 2010, at 1:35 PM, Chris Fields wrote: > >> Bio::Species had previously inherited from Bio::Taxon, but also required >> it to hold a Bio::Tree::Tree which contained a circular reference back >> to the Bio::Species object, thus requiring Scalar::Util::weaken. This >> has caused several hard-to-diagnose problems with premature garbage >> collection, including some issues with threads (bug 3017). > > > Is there something we should learn for future cases in which circular references are being considered with the S::U::weaken remedy (such as the recent one re: SeqI<->SeqFeatureI)? > > -hilmar In my experience, using weaken() is a bit of a 'code smell', and in general there are nice, sane ways to work around it. The solutions I outlined for the SeqI<->SeqFeatureI suggestion I thought made sense, if you think of Bio::SeqI as really more like a Bio::SeqRecord (has-a PrimarySeqI, does hold features, annotations, etc). There are no circular refs in this case: SeqI has-a SeqFeature(s)I, via FeatureHolderI SeqI has-a PrimarySeqI SeqFeatureI has-a PrimarySeqI Nothing refers back to SeqI It's a nice design decision and a great delegation of duties: SeqFeatures shouldn't need the Seq(Record) as a whole but the just the sequence itself, present as the PrimarySeqI, therefore they are attached to that. Any sequence-specific changes (methods, attributes) should therefore be in PrimarySeqI, and if needed could be delegated to for convenience from a relevant SeqI. In this particular instance (Bio::Species), there appeared to be a need to store a ref to the Tree (containing self) in self to implement the prior Bio::Species methods, thus requiring the use of weaken(). To me this was an indication that we really needed to rethink the design of the class. Maybe the containing instance (eg: Bio::Seq in this case) needs to hold the classification (as a Tree) and cache the relevant species NodeI (a Bio::Taxon). As we're still at the stage where we are using a Bio::Species, I pushed that functionality for the time being into the Bio::Species class: it has-a Bio::NodeI and a Bio::Tree::Tree, but neither refers back to the Bio::Species. We're planning on deprecating Bio::Species in future releases anyway, and reimplementing so that Bio::Seq is storing the Tree and the Bio::Taxon species node should be easy when the time comes. Actually, this probably suggests abstracting the simplest parts of that out into a common interface, which could be switched over to Bio::Seq when needed. May work on that a bit... chris From holland at eaglegenomics.com Mon Jul 5 10:06:56 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 5 Jul 2010 11:06:56 +0100 Subject: [Bioperl-l] Job opening at Eagle Message-ID: Hi all - thought this might be of interest to you. ==== Eagle Genomics is 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. With a number of exciting new projects on the horizon we're continuing to build up our team of talented and committed experts to help us deliver them. We are currently looking for a top-class developer to work on a wide range of complex projects. The role involves a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had at least 3 years prior experience developing code for bioinformatics projects. For this Perl/Ensembl role you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. Extensive experience programming in another language, particularly Java, is a bonus but not essential. In addition to your superb technical and customer service skills, you will also: * be able to communicate clearly and proactively, * 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, * be a self-starter and good at managing your own workload and responsibilities. You will also have had hands-on experience in at least two of the following: * SQL query design, * Open-source bioinformatics toolkits such as BioPerl, BioMart, BioSQL, etc., * Amazon EC2, * VMware, * Workflow/pipeline design (preferably using eHive or Taverna), * System and user documentation, * Developing and presenting training courses for users and developers. The successful candidate would be expected to work from our offices near Cambridge. 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. We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. The closing date is 23rd July. ==== cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From davila.marcela at gmail.com Mon Jul 5 12:57:01 2010 From: davila.marcela at gmail.com (Marcela Davila) Date: Mon, 5 Jul 2010 05:57:01 -0700 (PDT) Subject: [Bioperl-l] Infernal parser Message-ID: Hi there! I was wondering where I can set a different program directory (a local directory that has a different version of the Infernal package) rather than that specified in the ENV variable to run cmsearch while using Bio::Tools::Run::Infernal. Thanks! From cjfields at illinois.edu Mon Jul 5 15:19:13 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 10:19:13 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. chris On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > Hi there! > > I was wondering where I can set a different program directory (a local > directory that has a different version of the Infernal package) rather > than that specified in the ENV variable to run cmsearch while using > Bio::Tools::Run::Infernal. > > Thanks! > _______________________________________________ > 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 Jul 5 16:18:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jul 2010 11:18:30 -0500 Subject: [Bioperl-l] Infernal parser In-Reply-To: References: Message-ID: <0A2DAC96-808B-4583-B9F7-DBE44F9F9F86@illinois.edu> Marcela, After taking a look again and running a few local checks, I found that setting INFERNALDIR does work after all. I committed some code so that you can also explicitly set program_dir() as well, so the order of preference is: setting program_dir() > INFERNALDIR > PATH failing if an executable isn't found in any of those. That shouldn't be necessary, though (setting INFERNALDIR in your local env should suffice). Note that the Infernal wrapper only really supports Infernal 1.0 and up now, but the older releases still support pre-1.0 if you need them. chris On Jul 5, 2010, at 10:19 AM, Chris Fields wrote: > Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used. I can work on adding this in. > > chris > > On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote: > >> Hi there! >> >> I was wondering where I can set a different program directory (a local >> directory that has a different version of the Infernal package) rather >> than that specified in the ENV variable to run cmsearch while using >> Bio::Tools::Run::Infernal. >> >> Thanks! >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Tue Jul 6 12:37:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 6 Jul 2010 13:37:05 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl Message-ID: Hello, I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the set of scripts in BioPerl. Below is what I have so far. The script works by reading in a GFF of 'repeat_region's and a fasta file of sequences. It outputs a fasta sequence file with the repeats replaced by Xs. The script clearly needs to be more configurable, but I thought I'd send it along now to see if I'm working along the right lines, or if I should be using a different approach. Comments? Cheers, Dan. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $seq_file; my $gff_file; GetOptions ( "verbose" => \$verbose, "seq=s" => \$seq_file, "gff=s" => \$gff_file, ) or die "failed to parse command line options\n"; die "fail $gff_file : $!\n" unless -s $gff_file; ## Set up the BioPerl objects my $seq_reader = Bio::SeqIO->new( -file => $seq_file, -format => 'fasta' ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => 'fasta', -width => 80 ); my $gff_reader = Bio::FeatureIO->new( -file => $gff_file, -format => 'GFF', ); #warn $seq_reader->width, "\n"; exit; ## Run my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>1){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq 'repeat_region'){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } # Debugging #last if $c > 100; } warn "read $c repeat_region features for ", scalar keys(%repeats), " sequences\n"; ## while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; print length($sequence), "\n" if $verbose > 0; for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, 'X' x ($end - $start)); } print length($sequence), "\n" if $verbose > 0; $seq->seq($sequence); $seq_writer->write_seq($seq); # Debugging; #last; } warn "OK\n"; From armendarez77 at hotmail.com Tue Jul 6 14:23:55 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 07:23:55 -0700 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From sharmashalu.bio at gmail.com Tue Jul 6 14:48:58 2010 From: sharmashalu.bio at gmail.com (shalu sharma) Date: Tue, 6 Jul 2010 10:48:58 -0400 Subject: [Bioperl-l] Intergenomic sequences Message-ID: Hi All, This is not a bioperl question but i thought someone might know the answer. Is there any package/program to find intergenic sequences? I would really appreciate your help. Thanks Shalu From bosborne11 at verizon.net Tue Jul 6 14:36:18 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:36:18 +0200 Subject: [Bioperl-l] Get GIs from Taxonomy ID In-Reply-To: References: , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz> Message-ID: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: > > Hello, > > I'm designing degenerate primers using > Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 > Ns, but on some sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 6 14:50:25 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 06 Jul 2010 16:50:25 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: =head1 NAME bioflat_index.pl - index sequence files using Bio::DB::Flat =head1 DESCRIPTION Create or update a biological sequence database indexed with the Bio::DB::Flat indexing scheme. The arguments are a list of flat files containing the sequence information to be indexed. =head1 USAGE bioflat_index.pl file1 file2 file3... Options: --create Create or reinitialize the index. If not specified, the index must already exist. --format The format of the sequence files. Must be one of "genbank", "swissprot", "embl" or "fasta". --location Path to the directory in which the index files are stored. --dbname The symbolic name of the database to be created. --indextype Type of index to create. Either "bdb" or "flat". "binarysearch" is the same as "flat". Options can be abbreviated. For example, use -i for --indextype. The following environment variables will be used as defaults if the corresponding options are not provided: OBDA_FORMAT format of sequence file OBDA_LOCATION path to directory in which index files are stored OBDA_DBNAME name of database OBDA_INDEX type of index to create =cut On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > Hello, > > I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the > set of scripts in BioPerl. Below is what I have so far. The script > works by reading in a GFF of 'repeat_region's and a fasta file of > sequences. It outputs a fasta sequence file with the repeats replaced > by Xs. > > The script clearly needs to be more configurable, but I thought I'd > send it along now to see if I'm working along the right lines, or if I > should be using a different approach. > > Comments? > > > Cheers, > Dan. > > > > #!/usr/bin/perl -w > > use strict; > use Getopt::Long; > > use Bio::SeqIO; > use Bio::FeatureIO; > > > > ## Set options > > my $verbose = 0; > my $seq_file; > my $gff_file; > > GetOptions > ( > "verbose" => \$verbose, > "seq=s" => \$seq_file, > "gff=s" => \$gff_file, > ) > or die "failed to parse command line options\n"; > > die "fail $gff_file : $!\n" > unless -s $gff_file; > > > > ## Set up the BioPerl objects > > my $seq_reader = > Bio::SeqIO->new( -file => $seq_file, > -format => 'fasta' > ); > > my $seq_writer = > Bio::SeqIO->new( -fh => \*STDOUT, > -format => 'fasta', > -width => 80 > ); > > my $gff_reader = > Bio::FeatureIO->new( -file => $gff_file, > -format => 'GFF', > ); > > #warn $seq_reader->width, "\n"; exit; > > > > ## Run > > my (%repeats, $c); > > while ( my $feature = $gff_reader->next_feature() ) { > if($verbose>1){ > print > join("\t", #$feature, > $feature->seq_id, > $feature->type->name, > $feature->start, > $feature->end, > ), "\n"; > } > > if($feature->type->name eq 'repeat_region'){ > $c++; > push @{$repeats{ $feature->seq_id }}, > [$feature->start, > $feature->end]; > } > > # Debugging > #last if $c > 100; > } > > warn "read $c repeat_region features for ", > scalar keys(%repeats), " sequences\n"; > > > > ## > > while(my $seq = $seq_reader->next_seq){ > my $id = $seq->id; > my $sequence = $seq->seq; > > print $id, "\n" > if $verbose > 0; > > print length($sequence), "\n" > if $verbose > 0; > > for my $region (@{$repeats{ $id }}){ > my ($start, $end) = @$region; > print "$start\t$end\n" > if $verbose > 1; > > substr($sequence, $start, $end - $start, 'X' x ($end - $start)); > } > > print length($sequence), "\n" > if $verbose > 0; > > $seq->seq($sequence); > > $seq_writer->write_seq($seq); > > # Debugging; > #last; > } > > warn "OK\n"; > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From armendarez77 at hotmail.com Tue Jul 6 15:58:11 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 08:58:11 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: Hi Brian, This sort of worked. The script still dies with the same complaint when the primer sequence is 19 bases long and starts with an 'n': Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't look very DNA to me at .... However, other 19bp long sequences with 3 internal n's are allowed. Is there another way to prevent the script from dying when it comes across these sequences or should I just not allow these sequences to be processed? Thanks, Veronica Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com Veronica, Yes, when you're making your sequence object do something like: -alphabet => 'dna' For example: use Bio::Seq; $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 PM, wrote: Hello, I'm designing degenerate primers using Bio::Tools::Primer3 and Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some sequences the script dies with the following error: Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629. I couldn't find any information on this error. Is there a way to catch or override it? Thank you, Veronica _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From roy.chaudhuri at gmail.com Tue Jul 6 16:31:04 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 06 Jul 2010 17:31:04 +0100 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> Message-ID: <4C335A48.8000006@gmail.com> Hi Veronica, Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. Cheers. Roy. On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > > Hi Brian, > > This sort of worked. The script still dies with the same complaint > when the primer sequence is 19 bases long and starts with an 'n': > > Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > look very DNA to me at .... > > > However, other 19bp long sequences with 3 internal n's are allowed. > Is there another way to prevent the script from dying when it comes > across these sequences or should I just not allow these sequences to > be processed? > > Thanks, > > Veronica > > Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > > > > Veronica, Yes, when you're making your sequence object do something > like: -alphabet => 'dna' For example: use Bio::Seq; > > $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > PM, wrote: > Hello, > > I'm designing degenerate primers using Bio::Tools::Primer3 and > Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > sequences the script dies with the following error: > > Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > look very DNA to me at Perl.pm line 629. > > > > I couldn't find any information on this error. Is there a way to > catch or override it? > > Thank you, > > Veronica > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > Bioperl-l mailing list Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > > _______________________________________________ > 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 Jul 6 17:17:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 12:17:03 -0500 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <4C335A48.8000006@gmail.com> References: , , <1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net> <4C335A48.8000006@gmail.com> Message-ID: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! chris On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > Hi Veronica, > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > Cheers. > Roy. > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: >> >> Hi Brian, >> >> This sort of worked. The script still dies with the same complaint >> when the primer sequence is 19 bases long and starts with an 'n': >> >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't >> look very DNA to me at .... >> >> >> However, other 19bp long sequences with 3 internal n's are allowed. >> Is there another way to prevent the script from dying when it comes >> across these sequences or should I just not allow these sequences to >> be processed? >> >> Thanks, >> >> Veronica >> >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com >> >> >> >> Veronica, Yes, when you're making your sequence object do something >> like: -alphabet => 'dna' For example: use Bio::Seq; >> >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 >> PM, wrote: >> Hello, >> >> I'm designing degenerate primers using Bio::Tools::Primer3 and >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some >> sequences the script dies with the following error: >> >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't >> look very DNA to me at Perl.pm line 629. >> >> >> >> I couldn't find any information on this error. Is there a way to >> catch or override it? >> >> Thank you, >> >> Veronica >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _________________________________________________________________ >> Hotmail has tools for the New Busy. Search, chat and e-mail from your >> inbox. >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 >> >> > _______________________________________________ >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 6 18:21:10 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 6 Jul 2010 11:21:10 -0700 Subject: [Bioperl-l] 85% ATGCN In-Reply-To: <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> References: , ,,<1C8E211A-F676-47C4-AB24-E01F60C8F48E@sbc.su.se>, , , <18DF7D20DFEC044098A1062202F5FFF32DC257E462@exchsth.agresearch.co.nz>, , , , , , <18DF7D20DFEC044098A1062202F5FFF32DC257E4AA@exchsth.agresearch.co.nz>, , , , <859B6724-5DC1-487C-85E1-D1F6B56AB330@verizon.net>, , <4C335A48.8000006@gmail.com>, <1804F90A-5AEE-4FA7-8892-3400ECAFB0DF@illinois.edu> Message-ID: Thank you. The missing 'n' was the problem. Veronica > From: cjfields at illinois.edu > Date: Tue, 6 Jul 2010 12:17:03 -0500 > To: roy.chaudhuri at gmail.com > CC: bioperl-l at lists.open-bio.org; bosborne11 at verizon.net; armendarez77 at hotmail.com > Subject: Re: [Bioperl-l] 85% ATGCN > > Yeah, surprised that one didn't show up before. 'use strict' and perl 5.12 for the win! > > chris > > On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote: > > > Hi Veronica, > > > > Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th: > > http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664 > > > > So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit. > > > > Cheers. > > Roy. > > > > > > > > On 06/07/2010 16:58, armendarez77 at hotmail.com wrote: > >> > >> Hi Brian, > >> > >> This sort of worked. The script still dies with the same complaint > >> when the primer sequence is 19 bases long and starts with an 'n': > >> > >> Sequence [nGCnGTGCGTTGGTCnTTG] is less than 85% ATGCN, which doesn't > >> look very DNA to me at .... > >> > >> > >> However, other 19bp long sequences with 3 internal n's are allowed. > >> Is there another way to prevent the script from dying when it comes > >> across these sequences or should I just not allow these sequences to > >> be processed? > >> > >> Thanks, > >> > >> Veronica > >> > >> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID From: > >> bosborne11 at verizon.net Date: Tue, 6 Jul 2010 16:36:18 +0200 CC: > >> bioperl-l at lists.open-bio.org To: armendarez77 at hotmail.com > >> > >> > >> > >> Veronica, Yes, when you're making your sequence object do something > >> like: -alphabet => 'dna' For example: use Bio::Seq; > >> > >> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", > >> -alphabet => 'dna' ); Brian O. On Jul 6, 2010, at 4:23 > >> PM, wrote: > >> Hello, > >> > >> I'm designing degenerate primers using Bio::Tools::Primer3 and > >> Bio::Tools::Run::Primer3. I'm allowing up to 3 Ns, but on some > >> sequences the script dies with the following error: > >> > >> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't > >> look very DNA to me at Perl.pm line 629. > >> > >> > >> > >> I couldn't find any information on this error. Is there a way to > >> catch or override it? > >> > >> Thank you, > >> > >> Veronica > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >> > >> _________________________________________________________________ > >> Hotmail has tools for the New Busy. Search, chat and e-mail from your > >> inbox. > >> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > >> > >> > > _______________________________________________ > >> Bioperl-l mailing list Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/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 _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From kellert at ohsu.edu Tue Jul 6 21:54:36 2010 From: kellert at ohsu.edu (Tom Keller) Date: Tue, 6 Jul 2010 14:54:36 -0700 Subject: [Bioperl-l] SeqIO tag/location question Message-ID: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Greetings, A genbank file I am working with has features: exon 37167..37302 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=24 exon 39189..39256 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=25 exon 48058..50644 /gene="SLC12A3" /gene_synonym="FLJ96318; NCCT; TSC" /inference="alignment:Splign:1.39.8" /number=26 When I parse it using: my $db = Bio::DB::RefSeq->new(); my $seq = $db->get_Seq_by_acc($accession); my @features = $seq->get_SeqFeatures; for my$feat_obj ( @features ) { if ($feat_obj->primary_tag eq 'exon') { print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; for my $tag ($feat_obj->get_all_tags) { for my $value ($feat_obj->get_tag_values($tag)) { print " value: ", $value, "\n"; } } } } I get the following: primary tag: exon start: 42167 end: 42302 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 24 primary tag: exon start: 44189 end: 44256 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 25 primary tag: exon start: 53058 end: 55644 value: SLC12A3 value: FLJ96318; NCCT; TSC value: alignment:Splign:1.39.8 value: 26 Where does the discrepancy in location (+5000) come from? thanks for your help, Tom MMI DNA Services Core Facility 4-2442 kellert at ohsu.edu RJH (CROET/BasicScience) 6339b From cjfields at illinois.edu Tue Jul 6 23:10:18 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jul 2010 18:10:18 -0500 Subject: [Bioperl-l] SeqIO tag/location question In-Reply-To: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> References: <4C1F4BE1-1C21-4452-81E1-ADD965B29C9E@ohsu.edu> Message-ID: <0DBD5366-A92B-4A70-B882-7E8FA88A85B0@illinois.edu> RefSeq pulls the file from EBI, not from NCBI (IIRC), so maybe there is a difference between the two versions? Hard to say w/o knowing the exact accession. chris On Jul 6, 2010, at 4:54 PM, Tom Keller wrote: > Greetings, > A genbank file I am working with has features: > exon 37167..37302 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=24 > exon 39189..39256 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=25 > exon 48058..50644 > /gene="SLC12A3" > /gene_synonym="FLJ96318; NCCT; TSC" > /inference="alignment:Splign:1.39.8" > /number=26 > > When I parse it using: > my $db = Bio::DB::RefSeq->new(); > my $seq = $db->get_Seq_by_acc($accession); > my @features = $seq->get_SeqFeatures; > for my$feat_obj ( @features ) { > if ($feat_obj->primary_tag eq 'exon') { > print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n"; > for my $tag ($feat_obj->get_all_tags) { > for my $value ($feat_obj->get_tag_values($tag)) { > print " value: ", $value, "\n"; > } > } > } > } > > I get the following: > primary tag: exon start: 42167 end: 42302 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 24 > primary tag: exon start: 44189 end: 44256 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 25 > primary tag: exon start: 53058 end: 55644 > value: SLC12A3 > value: FLJ96318; NCCT; TSC > value: alignment:Splign:1.39.8 > value: 26 > > Where does the discrepancy in location (+5000) come from? > > thanks for your help, > Tom > MMI DNA Services Core Facility > 4-2442 > kellert at ohsu.edu > RJH (CROET/BasicScience) 6339b > > > > > > > _______________________________________________ > 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 Tue Jul 6 23:14:15 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 7 Jul 2010 00:14:15 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Cheers Brian! Do you think this script will work if I allow sequence and feature '-format's to be picked by the user among all those listed as valid file formats in BioPerl? http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS Or should I stick to Fasta/GFF (or some other implementation)? Cheers, Dan. On 6 July 2010 15:50, Brian Osborne wrote: > Dan, > > There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: > > =head1 NAME > > bioflat_index.pl - index sequence files using Bio::DB::Flat > > =head1 DESCRIPTION > > ?Create or update a biological sequence database indexed with the > ?Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files > ?containing the sequence information to be indexed. > > =head1 USAGE > > ?bioflat_index.pl file1 file2 file3... > > ?Options: > > ? ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, > ? ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. > > ? ? --format ? ? The format of the sequence files. ?Must be one > ? ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". > > ? ? --location ? ? Path to the directory in which the index files > ? ? ? ? ? ? ? ? ? ? ? ? ? are stored. > > ? ? --dbname ? ? ? The symbolic name of the database to be created. > > ? ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". > ? ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". > > Options can be abbreviated. ?For example, use -i for --indextype. > > The following environment variables will be used as defaults if the > corresponding options are not provided: > > ? ? OBDA_FORMAT ? ? ?format of sequence file > ? ? OBDA_LOCATION ? ?path to directory in which index files are stored > ? ? OBDA_DBNAME ? ? ?name of database > ? ? OBDA_INDEX ? ? ? type of index to create > > =cut > > > On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: > >> Hello, >> >> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >> set of scripts in BioPerl. Below is what I have so far. The script >> works by reading in a GFF of 'repeat_region's and a fasta file of >> sequences. It outputs a fasta sequence file with the repeats replaced >> by Xs. >> >> The script clearly needs to be more configurable, but I thought I'd >> send it along now to see if I'm working along the right lines, or if I >> should be using a different approach. >> >> Comments? >> >> >> Cheers, >> Dan. >> >> >> >> #!/usr/bin/perl -w >> >> use strict; >> use Getopt::Long; >> >> use Bio::SeqIO; >> use Bio::FeatureIO; >> >> >> >> ## Set options >> >> my $verbose = 0; >> my $seq_file; >> my $gff_file; >> >> GetOptions >> ?( >> ? "verbose" => \$verbose, >> ? "seq=s" => \$seq_file, >> ? "gff=s" => \$gff_file, >> ?) >> ?or die "failed to parse command line options\n"; >> >> die "fail $gff_file : $!\n" >> ?unless -s $gff_file; >> >> >> >> ## Set up the BioPerl objects >> >> my $seq_reader = >> ?Bio::SeqIO->new( -file => $seq_file, >> ? ? ? ? ? ? ? ? ?-format => 'fasta' >> ? ? ? ? ? ? ? ?); >> >> my $seq_writer = >> ?Bio::SeqIO->new( -fh => \*STDOUT, >> ? ? ? ? ? ? ? ? ?-format => 'fasta', >> ? ? ? ? ? ? ? ? ?-width => 80 >> ? ? ? ? ? ? ? ?); >> >> my $gff_reader = >> ?Bio::FeatureIO->new( -file => $gff_file, >> ? ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >> ? ? ? ? ? ? ? ? ? ?); >> >> #warn $seq_reader->width, "\n"; exit; >> >> >> >> ## Run >> >> my (%repeats, $c); >> >> while ( my $feature = $gff_reader->next_feature() ) { >> ?if($verbose>1){ >> ? ?print >> ? ? ?join("\t", #$feature, >> ? ? ? ? ?$feature->seq_id, >> ? ? ? ? ?$feature->type->name, >> ? ? ? ? ?$feature->start, >> ? ? ? ? ?$feature->end, >> ? ? ? ? ), "\n"; >> ?} >> >> ?if($feature->type->name eq 'repeat_region'){ >> ? ?$c++; >> ? ?push @{$repeats{ $feature->seq_id }}, >> ? ? ?[$feature->start, >> ? ? ? $feature->end]; >> ?} >> >> ?# Debugging >> ?#last if $c > 100; >> } >> >> warn "read $c repeat_region features for ", >> ?scalar keys(%repeats), " sequences\n"; >> >> >> >> ## >> >> while(my $seq = $seq_reader->next_seq){ >> ?my $id = $seq->id; >> ?my $sequence = $seq->seq; >> >> ?print $id, "\n" >> ? ?if $verbose > 0; >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?for my $region (@{$repeats{ $id }}){ >> ? ?my ($start, $end) = @$region; >> ? ?print "$start\t$end\n" >> ? ? ?if $verbose > 1; >> >> ? ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >> ?} >> >> ?print length($sequence), "\n" >> ? ?if $verbose > 0; >> >> ?$seq->seq($sequence); >> >> ?$seq_writer->write_seq($seq); >> >> ?# Debugging; >> ?#last; >> } >> >> warn "OK\n"; >> _______________________________________________ >> 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 Jul 7 09:42:59 2010 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 07 Jul 2010 11:42:59 +0200 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: Dan, In my opinion the user should be able to use any supported format as input, yes. Brian O. On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > Cheers Brian! > > Do you think this script will work if I allow sequence and feature > '-format's to be picked by the user among all those listed as valid > file formats in BioPerl? > > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats > http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS > > > Or should I stick to Fasta/GFF (or some other implementation)? > > Cheers, > Dan. > > > On 6 July 2010 15:50, Brian Osborne wrote: >> Dan, >> >> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >> >> =head1 NAME >> >> bioflat_index.pl - index sequence files using Bio::DB::Flat >> >> =head1 DESCRIPTION >> >> Create or update a biological sequence database indexed with the >> Bio::DB::Flat indexing scheme. The arguments are a list of flat files >> containing the sequence information to be indexed. >> >> =head1 USAGE >> >> bioflat_index.pl file1 file2 file3... >> >> Options: >> >> --create Create or reinitialize the index. If not specified, >> the index must already exist. >> >> --format The format of the sequence files. Must be one >> of "genbank", "swissprot", "embl" or "fasta". >> >> --location Path to the directory in which the index files >> are stored. >> >> --dbname The symbolic name of the database to be created. >> >> --indextype Type of index to create. Either "bdb" or "flat". >> "binarysearch" is the same as "flat". >> >> Options can be abbreviated. For example, use -i for --indextype. >> >> The following environment variables will be used as defaults if the >> corresponding options are not provided: >> >> OBDA_FORMAT format of sequence file >> OBDA_LOCATION path to directory in which index files are stored >> OBDA_DBNAME name of database >> OBDA_INDEX type of index to create >> >> =cut >> >> >> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >> >>> Hello, >>> >>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>> set of scripts in BioPerl. Below is what I have so far. The script >>> works by reading in a GFF of 'repeat_region's and a fasta file of >>> sequences. It outputs a fasta sequence file with the repeats replaced >>> by Xs. >>> >>> The script clearly needs to be more configurable, but I thought I'd >>> send it along now to see if I'm working along the right lines, or if I >>> should be using a different approach. >>> >>> Comments? >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> #!/usr/bin/perl -w >>> >>> use strict; >>> use Getopt::Long; >>> >>> use Bio::SeqIO; >>> use Bio::FeatureIO; >>> >>> >>> >>> ## Set options >>> >>> my $verbose = 0; >>> my $seq_file; >>> my $gff_file; >>> >>> GetOptions >>> ( >>> "verbose" => \$verbose, >>> "seq=s" => \$seq_file, >>> "gff=s" => \$gff_file, >>> ) >>> or die "failed to parse command line options\n"; >>> >>> die "fail $gff_file : $!\n" >>> unless -s $gff_file; >>> >>> >>> >>> ## Set up the BioPerl objects >>> >>> my $seq_reader = >>> Bio::SeqIO->new( -file => $seq_file, >>> -format => 'fasta' >>> ); >>> >>> my $seq_writer = >>> Bio::SeqIO->new( -fh => \*STDOUT, >>> -format => 'fasta', >>> -width => 80 >>> ); >>> >>> my $gff_reader = >>> Bio::FeatureIO->new( -file => $gff_file, >>> -format => 'GFF', >>> ); >>> >>> #warn $seq_reader->width, "\n"; exit; >>> >>> >>> >>> ## Run >>> >>> my (%repeats, $c); >>> >>> while ( my $feature = $gff_reader->next_feature() ) { >>> if($verbose>1){ >>> print >>> join("\t", #$feature, >>> $feature->seq_id, >>> $feature->type->name, >>> $feature->start, >>> $feature->end, >>> ), "\n"; >>> } >>> >>> if($feature->type->name eq 'repeat_region'){ >>> $c++; >>> push @{$repeats{ $feature->seq_id }}, >>> [$feature->start, >>> $feature->end]; >>> } >>> >>> # Debugging >>> #last if $c > 100; >>> } >>> >>> warn "read $c repeat_region features for ", >>> scalar keys(%repeats), " sequences\n"; >>> >>> >>> >>> ## >>> >>> while(my $seq = $seq_reader->next_seq){ >>> my $id = $seq->id; >>> my $sequence = $seq->seq; >>> >>> print $id, "\n" >>> if $verbose > 0; >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> for my $region (@{$repeats{ $id }}){ >>> my ($start, $end) = @$region; >>> print "$start\t$end\n" >>> if $verbose > 1; >>> >>> substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>> } >>> >>> print length($sequence), "\n" >>> if $verbose > 0; >>> >>> $seq->seq($sequence); >>> >>> $seq_writer->write_seq($seq); >>> >>> # Debugging; >>> #last; >>> } >>> >>> warn "OK\n"; >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From gb7 at sanger.ac.uk Wed Jul 7 14:41:13 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Wed, 07 Jul 2010 15:41:13 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes Message-ID: <4C349209.6030209@sanger.ac.uk> Hi. I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? Thanks. Greg. -- 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 heikki.lehvaslaiho at gmail.com Wed Jul 7 17:14:21 2010 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 7 Jul 2010 20:14:21 +0300 Subject: [Bioperl-l] BLAT Howto? In-Reply-To: References: Message-ID: There are BLAT and SSAHA that have been around for some time. For next gen sequences, there are more algorithms coming up all the time. Have a look at e.g. Li and Homer in Briefings in Bioinformatics "A survey of sequence alignment algorithms for next-generation sequencing". -Heikki On 28 June 2010 16:15, Minh Bui wrote: > Hi everyone, > I am new to Bioperl and perl itself and running perl on window 7. > > ?My job is to develop an application that can search through a ?database > with thousands of queries. BLAT is a ?best option (if you know any other > algorithm that can do this, please let me know). I have been searching > through Bioperl BLAT documentation and there is only one document for BLAT > but without example. > I am wondering if anyone has done BLAT using Bioperl, please show me how to > use BLAT in ?Bioperl. > > Thank you very much and sorry for my english. Its not my first language. > _______________________________________________ > 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 Jul 8 02:36:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jul 2010 21:36:22 -0500 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: It is possible our NEXUS parser doesn't do this for some reason, but we would need a sample file to work out the problem. You could try Rutger Vos's Bio::Phylo, which may have this working. chris On Jul 7, 2010, at 9:41 AM, Greg Baillie wrote: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors. > > In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values. > > Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values? > > Thanks. > > Greg. > > > > -- > 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. _______________________________________________ > 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 Jul 8 04:27:56 2010 From: jason at bioperl.org (Jason Stajich) Date: Wed, 07 Jul 2010 21:27:56 -0700 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C349209.6030209@sanger.ac.uk> References: <4C349209.6030209@sanger.ac.uk> Message-ID: <4C3553CC.8030400@bioperl.org> Hi - Is this just that you have internal nodes labeled with the bootstrap/posterior value? If so you just want the node ids for the internal nodes then. The semantics of what is encoded in the internal nodes is not forced by the nexus format so it assumes they are ids by default. You can call $tree->move_id_to_bootstrap to migrate the ids of internal nodes to the bootstrap option. you can also use the -internal_node_id => 'bootstrap' option when initializing TreeIO objects too: =head2 new Title : new Usage : my $obj = Bio::TreeIO->new(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args : a hash. useful keys: -format : Specify the format of the file. Supported formats: newick Newick tree format nexus Nexus tree format nhx NHX tree format svggraph SVG graphical representation of tree tabtree ASCII text representation of tree lintree lintree output format -internal_node_id : what is stored in the internal node ids, bootstrap values or ids, coded as 'bootstrap' or 'id' -jason Greg Baillie wrote, On 7/7/10 7:41 AM: > Hi. > > I'm trying to extract information (eg. posterior values) from nodes of > trees generated using BEAST/treeannotator/FigTree. > > The trees, which are in nexus format, seem to load OK, but when I > iterate through the nodes looking for posterior values (/if ( > $node->has_tag('posterior') ) {.../), none of the nodes seem to have > posteriors. > > In fact, none of the nodes have any tags (/my @tags = > $node->get_all_tags(); print join ',', @tags/). And when I dump an > entire tree using Data::Dumper, there is no sign of any of the node > values. > > Does TreeIO handle these values? If so, should I be looking somewhere > other than the tags for the values? > > Thanks. > > Greg. From gb7 at sanger.ac.uk Thu Jul 8 14:24:14 2010 From: gb7 at sanger.ac.uk (Greg Baillie) Date: Thu, 08 Jul 2010 15:24:14 +0100 Subject: [Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes In-Reply-To: <4C3553CC.8030400@bioperl.org> References: <4C349209.6030209@sanger.ac.uk> <4C3553CC.8030400@bioperl.org> Message-ID: <4C35DF8E.1050905@sanger.ac.uk> Hi Jason. I'm trying to get access to the posterior probability value, rate, etc, that are stored within open-square-bracket-ampersand and close-square-bracket ([&]) blocks in the tree string. It appears that this information is stripped out during the parsing of the tree string (I have tried to get it from the $node->bootstrap()). I'm having trouble identifying the module that parses the tree string - I thought I might be able to modify that. Any suggestions where I might find the appropriate code? In the meantime, I'll look at the Bio::Phylo modules (as per Chris' suggestion) to see if they have a way of handling that info. Thanks. Greg. Jason Stajich wrote: > Hi - > > Is this just that you have internal nodes labeled with the > bootstrap/posterior value? If so you just want the node ids for the > internal nodes then. The semantics of what is encoded in the internal > nodes is not forced by the nexus format so it assumes they are ids by > default. > You can call $tree->move_id_to_bootstrap > to migrate the ids of internal nodes to the bootstrap option. > > you can also use the -internal_node_id => 'bootstrap' option when > initializing TreeIO objects too: > > =head2 new > > Title : new > Usage : my $obj = Bio::TreeIO->new(); > Function: Builds a new Bio::TreeIO object > Returns : Bio::TreeIO > Args : a hash. useful keys: > -format : Specify the format of the file. Supported formats: > > newick Newick tree format > nexus Nexus tree format > nhx NHX tree format > svggraph SVG graphical representation of tree > tabtree ASCII text representation of tree > lintree lintree output format > -internal_node_id : what is stored in the internal node ids, > bootstrap values or ids, coded as > 'bootstrap' or 'id' > > -jason > Greg Baillie wrote, On 7/7/10 7:41 AM: >> Hi. >> >> I'm trying to extract information (eg. posterior values) from nodes >> of trees generated using BEAST/treeannotator/FigTree. >> >> The trees, which are in nexus format, seem to load OK, but when I >> iterate through the nodes looking for posterior values (/if ( >> $node->has_tag('posterior') ) {.../), none of the nodes seem to have >> posteriors. >> >> In fact, none of the nodes have any tags (/my @tags = >> $node->get_all_tags(); print join ',', @tags/). And when I dump an >> entire tree using Data::Dumper, there is no sign of any of the node >> values. >> >> Does TreeIO handle these values? If so, should I be looking somewhere >> other than the tags for the values? >> >> Thanks. >> >> Greg. -- 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 dan.bolser at gmail.com Thu Jul 8 14:33:19 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 15:33:19 +0100 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) Message-ID: The bugtracker seems broken (or taking a painfully long time to log me in). So here is my bug report before I forget: Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace Body: The code had inconsistent use of the '_qualify' function, and one instance of a hard-coded table name. These issues were not apparent until "-namespace anything" was used. First I got the fatal error: DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 428, line 2. which was due to a hard-coded table name. Then, after fixing, I got the error: Loading bulk data into database...DBD::mysql::db do failed: Table 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 570, line 10000. i.e. the prefix was being added to the table name twice. I went through the code and tried to make all references to table names consistent to ensure that bugs like this won't creep in again... however, the code for this module isn't very consistent. (See patch attached). -------------- next part -------------- A non-text attachment was scrubbed... Name: mysql.pm.patch Type: text/x-patch Size: 11908 bytes Desc: not available URL: From dan.bolser at gmail.com Thu Jul 8 16:06:59 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 8 Jul 2010 17:06:59 +0100 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) Message-ID: Editing subject to see if it gets through... On 8 July 2010 15:33, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > From lincoln.stein at gmail.com Thu Jul 8 16:24:38 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:24:38 -0400 Subject: [Bioperl-l] Bug in Bio::DB::SeqFeature::Store::DBI::mysql.pm (attached patch) In-Reply-To: References: Message-ID: My code is never very consistent, unfortunately. Thanks for the patch, but it wasn't attached to the forwarded email. Could you try again? Lincoln On Thu, Jul 8, 2010 at 12:06 PM, Dan Bolser wrote: > Editing subject to see if it gets through... > > On 8 July 2010 15:33, Dan Bolser wrote: > > The bugtracker seems broken (or taking a painfully long time to log me > > in). So here is my bug report before I forget: > > > > > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > > > Body: > > The code had inconsistent use of the '_qualify' function, and one > > instance of a hard-coded table name. These issues were not apparent > > until "-namespace anything" was used. > > > > First I got the fatal error: > > > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 428, line 2. > > > > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > > > Loading bulk data into database...DBD::mysql::db do failed: Table > > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > > line 570, line 10000. > > > > > > i.e. the prefix was being added to the table name twice. > > > > > > I went through the code and tried to make all references to table > > names consistent to ensure that bugs like this won't creep in again... > > however, the code for this module isn't very consistent. > > > > (See patch attached). > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform 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 Thu Jul 8 16:28:14 2010 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 8 Jul 2010 12:28:14 -0400 Subject: [Bioperl-l] Bug in Bio/DB/SeqFeature/Store/DBI/mysql.pm (attached patch) In-Reply-To: References: Message-ID: Never mind. I found the patch in the earlier message. Thanks again for tracking down the issues. Lincoln On Thu, Jul 8, 2010 at 10:33 AM, Dan Bolser wrote: > The bugtracker seems broken (or taking a painfully long time to log me > in). So here is my bug report before I forget: > > > > Title: Found a few bugs in bp_seqfeature_load.PLS when using -namespace > > Body: > The code had inconsistent use of the '_qualify' function, and one > instance of a hard-coded table name. These issues were not apparent > until "-namespace anything" was used. > > First I got the fatal error: > > DBD::mysql::st execute failed: Table 'dbolser.feature' doesn't exist > at /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 428, line 2. > > > which was due to a hard-coded table name. Then, after fixing, I got the > error: > > Loading bulk data into database...DBD::mysql::db do failed: Table > 'dbolser.sheng_kai_sheng_kai_name' doesn't exist at > /homes/dbolser/perl5/lib/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm > line 570, line 10000. > > > i.e. the prefix was being added to the table name twice. > > > I went through the code and tried to make all references to table > names consistent to ensure that bugs like this won't creep in again... > however, the code for this module isn't very consistent. > > (See patch attached). > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From David.Messina at sbc.su.se Thu Jul 8 18:27:13 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jul 2010 14:27:13 -0400 Subject: [Bioperl-l] added -type for Bio::Annotation::DBLink Message-ID: Hi everybody, In working on representing sequence metadata*, I've found it useful to track the type of information that is involved in a database cross-reference. I'm adding an optional -type property to Bio::Annotation::DBLink to support this cleanly in BioPerl. Here follows my rationale. I'm not tied to doing this in B:A::DBLink if there's a better way ? it just seems the best route to me at the moment. -- So, what do I mean by tracking the type of information in a DB crossreference? Right now, a standard DBLink contains database => RefSeq ID => NM_12345 along with a few other optional properties. See the docs for details: http://doc.bioperl.org/bioperl-live/Bio/Annotation/DBLink.html I want to be able to say database => RefSeq ID => NM_12345 type => RNA Why? Two reasons: 1. a single database can store more than one type of information. RefSeq, for example, stores RNA and protein records. Although RefSeq's IDs are named intelligently to note their type (NM_xxx for transcript, NP_xxx for protein), this is not true for all databases and not everybody knows the ID codes. For example, here are three database-ID pairs: Genbank: AK291692.1 Genbank: CH471055.1 Genbank: AAH14616.1 Those are three different record types (mRNA, genomic DNA, protein) from the same database. 2. There can be multiple crossreferences for multiple types of information. There can be multiple source databases providing the same type of crossreference and multiple types of crossreferences. Take this example: Genbank: AAA81779.1 EMBL: AK291692 Ensembl: ENST00000308775 HPA: CAB001960 Two of these are mRNA records, one is a protein record, and one is something else entirely. If I wanted to take one mRNA xref and one protein xref from this set, I couldn't do it using solely the information provided above. If I had type information, though, it'd be easy. And since -type is an optional parameter, it is fully backwards-compatible. Any thoughts or comments? Dave * specifically, in SeqXML. See http://seqxml.org and http://doc.bioperl.org/bioperl-live/Bio/SeqIO/seqxml.html From abhishek.vit at gmail.com Fri Jul 9 15:02:09 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jul 2010 11:02:09 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO Message-ID: Hi (Chris) I feel I might be hitting a bug or missing something. I am trying to convert a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO for more clarity. I think the quality line is missing and the read is breaking into two lines. Any obvious mistakes ? Thanks! -Abhi ## Reading the FASTQ ASCII-64 file my $in = Bio::SeqIO->new( -format => 'fastq', -variant => 'illumina', -file => "<$in_fastq_file", ); ## File Handle for writing ASCII-33 (sanger) standard format my $out = Bio::SeqIO->new ( -format => 'fastq', -variant => 'sanger', -file => ">$out_fastq_file", ); while (my $oneread = $in->next_seq){ $out->write_seq($oneread); } Output: >HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCA AGGATATTGGTCTAA Input: @HWI-EAS397_0006:6:1:1023:19461#0/1 ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCAAGGATATTGGTCTAA +HWI-EAS397_0006:6:1:1023:19461#0/1 ^aYa^\a^aaaa\]a^^^^^]]]^L^Y]]]aa\`YZ^a]]a[a^^^^^`I^^^`]aaaa]]^]R`W^``^BBBBB From snoze.pa at gmail.com Fri Jul 9 19:06:31 2010 From: snoze.pa at gmail.com (snoze pa) Date: Fri, 9 Jul 2010 14:06:31 -0500 Subject: [Bioperl-l] MSG: Unrecognized DBSOURCE data: pdb: molecule Message-ID: Dear Users, While adding a genebank file to bioperl biosql database i am getting following error. Any Idea or help will be highly appreciated. Thank you s --------------------- WARNING --------------------- MSG: Unrecognized DBSOURCE data: pdb: molecule From biopython at maubp.freeserve.co.uk Sat Jul 10 11:43:47 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:43:47 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: > Hi (Chris) > > I feel I might be hitting a bug or missing something. I am trying to convert > a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO > for more clarity. I think the quality line is missing and the read is > breaking into two lines. > > Any obvious mistakes ? > > Thanks! > -Abhi It looks like you are getting FASTQ out rather than FASTQ (notice in addition to missing the qualities, the record starts with ">" rather than "@". Strange, as you do seem to be using the right FASTQ format and variant names. You could try using format="fastq-sanger" and format="fastq-illumina" rather than setting variant, to see if that changes anything. Peter From biopython at maubp.freeserve.co.uk Sat Jul 10 11:44:48 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sat, 10 Jul 2010 12:44:48 +0100 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: > On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >> Hi (Chris) >> >> I feel I might be hitting a bug or missing something. I am trying to convert >> a raw FASTQ from ASCII-64 to ASCII-33. ?I am copying the actual code and IO >> for more clarity. I think the quality line is missing and the read is >> breaking into two lines. >> >> Any obvious mistakes ? >> >> Thanks! >> -Abhi > > It looks like you are getting FASTQ out rather than FASTQ (notice in addition to > missing the qualities, the record starts with ">" rather than "@". Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) Peter From cjfields at illinois.edu Sat Jul 10 19:23:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jul 2010 14:23:30 -0500 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: On Jul 10, 2010, at 6:44 AM, Peter wrote: > On Sat, Jul 10, 2010 at 12:43 PM, Peter wrote: >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap wrote: >>> Hi (Chris) >>> >>> I feel I might be hitting a bug or missing something. I am trying to convert >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO >>> for more clarity. I think the quality line is missing and the read is >>> breaking into two lines. >>> >>> Any obvious mistakes ? >>> >>> Thanks! >>> -Abhi >> >> It looks like you are getting FASTQ out rather than FASTQ (notice in addition to >> missing the qualities, the record starts with ">" rather than "@". > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close together ;) > > Peter You have to be using a version of BioPerl that supports this. The previous version of the FASTQ parser released prior to refactoring returned FASTA when using write_seq(), which was a significant bug that was fixed during the complete overhaul prior to the FASTQ paper. My guess is the version of BioPerl is old and this is the module version being used. chris PS - Peter, had several very good mentions of this work from all Bio*/EMBOSS talks at BOSC, so a great success! From abhishek.vit at gmail.com Sat Jul 10 20:38:06 2010 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Sat, 10 Jul 2010 16:38:06 -0400 Subject: [Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO In-Reply-To: References: Message-ID: Thanks guys. Time to update my Bioperl. I will do that and report if I face issues. -A On Sat, Jul 10, 2010 at 3:23 PM, Chris Fields wrote: > On Jul 10, 2010, at 6:44 AM, Peter wrote: > > > On Sat, Jul 10, 2010 at 12:43 PM, Peter > wrote: > >> On Fri, Jul 9, 2010 at 4:02 PM, Abhishek Pratap > wrote: > >>> Hi (Chris) > >>> > >>> I feel I might be hitting a bug or missing something. I am trying to > convert > >>> a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code > and IO > >>> for more clarity. I think the quality line is missing and the read is > >>> breaking into two lines. > >>> > >>> Any obvious mistakes ? > >>> > >>> Thanks! > >>> -Abhi > >> > >> It looks like you are getting FASTQ out rather than FASTQ (notice in > addition to > >> missing the qualities, the record starts with ">" rather than "@". > > > > Typo: FASTA out rather than FASTQ. The A and Q keys are too close > together ;) > > > > Peter > > You have to be using a version of BioPerl that supports this. The previous > version of the FASTQ parser released prior to refactoring returned FASTA > when using write_seq(), which was a significant bug that was fixed during > the complete overhaul prior to the FASTQ paper. My guess is the version of > BioPerl is old and this is the module version being used. > > chris > > PS - Peter, had several very good mentions of this work from all > Bio*/EMBOSS talks at BOSC, so a great success! From pengyu.ut at gmail.com Sun Jul 11 01:40:47 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sat, 10 Jul 2010 20:40:47 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) Message-ID: Hi, I have the following warnings and perl program. I don't understand why there is a warning and what the error is. The ncbi's eutils url seems OK. If shrink $term (see the code), then the warning is gone. Could somebody let me know what the problem is with my bioperl code? http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 $ ./main.pl |head --------------------- WARNING --------------------- MSG: NCBI esearch Errors/Warnings: Error : --------------------------------------------------- 241 2412410 20616305 20581223 20572313 20564721 20554763 20542744 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::DB::EUtilities; my $factory = Bio::DB::EUtilities->new( -eutil => 'esearch', -db => 'pubmed', -email => 'mymail at foo.bar', #-term => 'anoxia[mh] AND neoplasms[mh]', #-term => 'small ubiquitin-related modifier proteins[mh]', -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR hCaCC-1[tiab]', #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink $term, then the warning is gone. -retmode => 'xml', -retmax => 1000000, ); print $factory->get_retmax,"\n"; print $factory->get_Response->content; -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 15:14:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 10:14:54 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: Message-ID: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > Hi, > > I have the following warnings and perl program. I don't understand why > there is a warning and what the error is. The ncbi's eutils url seems > OK. If shrink $term (see the code), then the warning is gone. Could > somebody let me know what the problem is with my bioperl code? > > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 > > $ ./main.pl |head > > --------------------- WARNING --------------------- > MSG: NCBI esearch Errors/Warnings: > Error : > --------------------------------------------------- > 241 > > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> > 2412410 > 20616305 > 20581223 > 20572313 > 20564721 > 20554763 > 20542744 > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::DB::EUtilities; > > my $factory = Bio::DB::EUtilities->new( > -eutil => 'esearch', > -db => 'pubmed', > -email => 'mymail at foo.bar', > #-term => 'anoxia[mh] AND neoplasms[mh]', > #-term => 'small ubiquitin-related modifier proteins[mh]', > -term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] > OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR > hCaCC-1[tiab]', > #-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink > $term, then the warning is gone. > -retmode => 'xml', > -retmax => 1000000, > ); > > print $factory->get_retmax,"\n"; > print $factory->get_Response->content; > > > -- > Regards, > Peng The above XML output from that query isn't complete; you left out: CLCRG1[tiab]FLJ95147[tiab] It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. I can take a look, but the error is pretty obvious from that output (can't find those phrases). chris From pengyu.ut at gmail.com Sun Jul 11 19:54:20 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 14:54:20 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 10:14 AM, Chris Fields wrote: > On Jul 10, 2010, at 8:40 PM, Peng Yu wrote: > >> Hi, >> >> I have the following warnings and perl program. I don't understand why >> there is a warning and what the error is. The ncbi's eutils url seems >> OK. If shrink $term (see the code), then the warning is gone. Could >> somebody let me know what the problem is with my bioperl code? >> >> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CLCA1[tiab]+OR+CACC[tiab]+OR+CACC1[tiab]+OR+CLCRG1[tiab]+OR+CaCC-1[tiab]+OR+FLJ95147[tiab]+OR+GOB5[tiab]+OR+hCLCA1[tiab]+OR+hCaCC-1[tiab]&retmax=1000 >> >> $ ./main.pl |head >> >> --------------------- WARNING --------------------- >> MSG: NCBI esearch Errors/Warnings: >> Error : >> --------------------------------------------------- >> 241 >> >> > 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd"> >> 2412410 >> ? ? ? ? ? ? ? 20616305 >> ? ? ? ? ? ? ? 20581223 >> ? ? ? ? ? ? ? 20572313 >> ? ? ? ? ? ? ? 20564721 >> ? ? ? ? ? ? ? 20554763 >> ? ? ? ? ? ? ? 20542744 >> $ cat main.pl >> #!/usr/bin/env perl >> >> use strict; >> use warnings; >> use Bio::DB::EUtilities; >> >> my $factory = Bio::DB::EUtilities->new( >> ?-eutil => 'esearch', >> ?-db => 'pubmed', >> ?-email => 'mymail at foo.bar', >> ?#-term => 'anoxia[mh] AND neoplasms[mh]', >> ?#-term => 'small ubiquitin-related modifier proteins[mh]', >> ?-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab] OR CLCRG1[tiab] >> OR CaCC-1[tiab] OR FLJ95147[tiab] OR GOB5[tiab] OR hCLCA1[tiab] OR >> hCaCC-1[tiab]', >> ?#-term => 'CLCA1[tiab] OR CACC[tiab] OR CACC1[tiab]', #if I shrink >> $term, then the warning is gone. >> ?-retmode => 'xml', >> ?-retmax => 1000000, >> ); >> >> print $factory->get_retmax,"\n"; >> print $factory->get_Response->content; >> >> >> -- >> Regards, >> Peng > > The above XML output from that query isn't complete; you left out: > > CLCRG1[tiab]FLJ95147[tiab] > > It's possible NCBI has changed the tags of their XML for esearch so the BioPerl parser isn't catching the error for some reason when an error is detected. ?I can take a look, but the error is pretty obvious from that output (can't find those phrases). Is there a way to suppress such error and warning message as they are not interesting to me? (As I can always check how many pubmed ids returned to determine if the search results anything). -- Regards, Peng From cjfields at illinois.edu Sun Jul 11 21:16:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 16:16:15 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> Message-ID: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > ... > Is there a way to suppress such error and warning message as they are > not interesting to me? (As I can always check how many pubmed ids > returned to determine if the search results anything). > > -- > Regards, > Peng Setting -verbose to -1 should work. chris From pengyu.ut at gmail.com Mon Jul 12 00:04:30 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 19:04:30 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > >> ... >> Is there a way to suppress such error and warning message as they are >> not interesting to me? (As I can always check how many pubmed ids >> returned to determine if the search results anything). >> >> -- >> Regards, >> Peng > > Setting -verbose to -1 should work. I don't see such an option in perldoc Bio::DB::EUtilities. Would you please let me know where it is documented? In fact, I don't see the document for new() in Bio::DB::EUtilities. Would you please add this to the document? Thank you! -- Regards, Peng From cjfields at illinois.edu Mon Jul 12 00:49:37 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 19:49:37 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <98EC5021-C5BC-4568-8080-99AC1C0C95A1@illinois.edu> On Jul 11, 2010, at 7:04 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields wrote: >> >> On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: >> >>> ... >>> Is there a way to suppress such error and warning message as they are >>> not interesting to me? (As I can always check how many pubmed ids >>> returned to determine if the search results anything). >>> >>> -- >>> Regards, >>> Peng >> >> Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng verbose() is a Bio::Root::Root/RootI method (all BioPerl classes inherit it), so that's the place to look. As for new(), yes I can work on that. chris From Russell.Smithies at agresearch.co.nz Mon Jul 12 01:08:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 13:08:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Take a look at the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities Details all the methods including those that are inherited. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peng Yu > Sent: Monday, 12 July 2010 12:05 p.m. > To: Chris Fields > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 4:16 PM, Chris Fields > wrote: > > > > On Jul 11, 2010, at 2:54 PM, Peng Yu wrote: > > > >> ... > >> Is there a way to suppress such error and warning message as they are > >> not interesting to me? (As I can always check how many pubmed ids > >> returned to determine if the search results anything). > >> > >> -- > >> Regards, > >> Peng > > > > Setting -verbose to -1 should work. > > I don't see such an option in perldoc Bio::DB::EUtilities. Would you > please let me know where it is documented? In fact, I don't see the > document for new() in Bio::DB::EUtilities. Would you please add this > to the document? Thank you! > > -- > Regards, > Peng > _______________________________________________ > 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 pengyu.ut at gmail.com Mon Jul 12 01:15:46 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Sun, 11 Jul 2010 20:15:46 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell wrote: > Take a look at the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > > Details all the methods including those that are inherited. This is every useful when l look for an inherent method. The box titled "methods for Bio::DB::EUtilities" is too small. May I suggest to make it a little bigger? Also, the box above it takes too much space, it is better to shrink it since there in only one class. Would you please help improve the appearance a little? -- Regards, Peng From cjfields at illinois.edu Mon Jul 12 03:45:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jul 2010 22:45:48 -0500 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > wrote: >> Take a look at the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&sort_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities >> >> Details all the methods including those that are inherited. > > This is every useful when l look for an inherent method. The box > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > to make it a little bigger? Also, the box above it takes too much > space, it is better to shrink it since there in only one class. Would > you please help improve the appearance a little? > > -- > Regards, > Peng Patches welcome chris From Russell.Smithies at agresearch.co.nz Mon Jul 12 04:07:28 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:07:28 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> I think you mean "on your PC the box is too small". Because BioPerl is cross-platform it shouldn't be customized to look best on specific hardware or software , for example, Windows 7 with IE9. The Deobfuscator is included in BioPerl so you are free to edit and run on your own web-server with colors and styles to suit your exacting tastes. And as Chris said, if you'd like added documentation or a web interface changed so it looks better on your PC I suggest you start writing some patches. Don't forget, the BioPerl developers are all volunteers and don't work for you!! --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Monday, 12 July 2010 3:46 p.m. > To: Peng Yu > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Jul 11, 2010, at 8:15 PM, Peng Yu wrote: > > > On Sun, Jul 11, 2010 at 8:08 PM, Smithies, Russell > > wrote: > >> Take a look at the deobfuscator: > >> http://bioperl.org/cgi- > bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ADB%3A%3AEUtilities&so > rt_order=by+method&search_string=Bio%3A%3ADB%3A%3AEUtilities > >> > >> Details all the methods including those that are inherited. > > > > This is every useful when l look for an inherent method. The box > > titled "methods for Bio::DB::EUtilities" is too small. May I suggest > > to make it a little bigger? Also, the box above it takes too much > > space, it is better to shrink it since there in only one class. Would > > you please help improve the appearance a little? > > > > -- > > Regards, > > Peng > > Patches welcome > > chris ======================================================================= 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 Russell.Smithies at agresearch.co.nz Mon Jul 12 04:27:02 2010 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Jul 2010 16:27:02 +1200 Subject: [Bioperl-l] No error message is given for a warning (EUtilities) In-Reply-To: References: <2E2E79D6-24EE-46A3-B968-B522CC3A53D6@illinois.edu> <3DB3011D-F8FC-4BB5-9840-3D08D63A45A3@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF32E7BC346AA@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF32E7BC347D6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32E7BC347F6@exchsth.agresearch.co.nz> It's all a matter of priorities and I can't see how increasing the number of rows displayed in a web interface is more important than any other items on the list http://www.bioperl.org/wiki/Project_priority_list If you feel strongly about it and you can justify the changes then submit a bug report, and a patch. --Russell > -----Original Message----- > From: Peng Yu [mailto:pengyu.ut at gmail.com] > Sent: Monday, 12 July 2010 4:15 p.m. > To: Smithies, Russell > Subject: Re: [Bioperl-l] No error message is given for a warning > (EUtilities) > > On Sun, Jul 11, 2010 at 11:07 PM, Smithies, Russell > wrote: > > I think you mean "on your PC the box is too small". > > Because BioPerl is cross-platform it shouldn't be customized to look > best on specific hardware or software , for example, Windows 7 with IE9. > > The Deobfuscator is included in BioPerl so you are free to edit and run > on your own web-server with colors and styles to suit your exacting > tastes. > > > > And as Chris said, if you'd like added documentation or a web interface > changed so it looks better on your PC I suggest you start writing some > patches. > > Don't forget, the BioPerl developers are all volunteers and don't work > for you!! > > This is just a suggestion. Do you think that this is an order? I > didn't mean so. My believe is that if I feel something can be > improved, maybe others think so as well. So I'm make the suggestions > for other users as well. > > You don't have to reply if it can not be done. > > -- > Regards, > Peng ======================================================================= 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 dan.bolser at gmail.com Mon Jul 12 09:34:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 10:34:47 +0100 Subject: [Bioperl-l] Suggestion for a new script: bp_repeat_mask_sequence.pl In-Reply-To: References: Message-ID: OK, here is my final version. I have tested it with GFF / Fasta, and in theory it works with all installed BioPerl sequence / feature file formats, however, I haven't tested any of those. #!/usr/bin/perl -w use strict; use Getopt::Long; use Bio::SeqIO; use Bio::FeatureIO; ## Set options my $verbose = 0; my $feature_file; my $sequence_file; my $feature_format = 'GFF'; my $sequence_format = 'Fasta'; my $feature_to_mask = 'repeat_region'; my $seq_mask_character = 'X'; GetOptions ( "verbose" => \$verbose, "feature_file|f=s" => \$feature_file, "sequence_file|s=s" => \$sequence_file, "feature_format|ff=s" => \$feature_format, "sequence_format|sf=s" => \$sequence_format, "feature_to_mask|m=s" => \$feature_to_mask, "seq_mask_character|c=s" => \$seq_mask_character, ) or die "failed to parse command line options\n"; ## Check options ## A value should be passed die usage() unless $sequence_file && $feature_file; ## The files should exist die "problem with feature file '$feature_file' : $!\n" unless -s $feature_file; die "problem with sequence file '$sequence_file' : $!\n" unless -s $sequence_file; ## The formats should be valid $feature_format = lc($feature_format); die "ERROR: feature format '$feature_format' is not supported!\n\n" unless eval( "require Bio::FeatureIO::$feature_format" ); $sequence_format = lc($sequence_format); die "ERROR: sequence format '$sequence_format' is not supported!\n\n" unless eval( "require Bio::SeqIO::$sequence_format" ); ## Erm... die "1: what are you trying to do?\n" unless $feature_to_mask; die "2: what are you trying to do?\n" unless length($seq_mask_character) == 1; =head1 NAME bp_repeat_mask_sequence.pl - mask sequence features =head1 DESCRIPTION Takes an input sequence file and a feature file, and returns the sequence with 'repeat_region' features masked out (replaced with X's). This is useful for downstream processing of the sequence file. The masked sequence is written to STDOUT. =head1 USAGE bp_repeat_mask_sequence.pl Options: -f --feature_file The file from which the sequence features will be read (for subsequent masking). -s --sequence_file The sequence file (to be masked). --ff --feature_format The format of the feature file (the default is GFF). --sf --sequence_format The format of the sequence file (the default is fasta). -m --feature_to_mask The type of feature to mask (the default is 'repeat_region'). -c --seq_mask_character The 'mask' character to use in the sequence. (the default is 'X'). -v --verbose Generate some debugging output =cut ## Set up the BioPerl objects my $gff_reader = Bio::FeatureIO->new( -file => $feature_file, -format => $feature_format ); my $seq_reader = Bio::SeqIO->new( -file => $sequence_file, -format => $sequence_format, ); my $seq_writer = Bio::SeqIO->new( -fh => \*STDOUT, -format => $sequence_format, ); ## Run warn "hashing features to mask\n"; my (%repeats, $c); while ( my $feature = $gff_reader->next_feature() ) { if($verbose>0){ print join("\t", #$feature, $feature->seq_id, $feature->type->name, $feature->start, $feature->end, ), "\n"; } if($feature->type->name eq $feature_to_mask){ $c++; push @{$repeats{ $feature->seq_id }}, [$feature->start, $feature->end]; } } warn "read $c '$feature_to_mask' features for ", scalar keys(%repeats), " sequences\n"; warn "masking sequences\n"; while(my $seq = $seq_reader->next_seq){ my $id = $seq->id; my $sequence = $seq->seq; print $id, "\n" if $verbose > 0; ## Do the masking for my $region (@{$repeats{ $id }}){ my ($start, $end) = @$region; print "$start\t$end\n" if $verbose > 1; substr($sequence, $start, $end - $start, $seq_mask_character x ($end - $start) ); } $seq->seq($sequence); $seq_writer->write_seq($seq); } warn "done\n"; # A bit of a hack: sub usage{ `perldoc -T ./$0` } On 7 July 2010 10:42, Brian Osborne wrote: > Dan, > > In my opinion the user should be able to use any supported format as input, yes. > > Brian O. > > On Jul 7, 2010, at 1:14 AM, Dan Bolser wrote: > >> Cheers Brian! >> >> Do you think this script will work if I allow sequence and feature >> '-format's to be picked by the user among all those listed as valid >> file formats in BioPerl? >> >> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats >> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/FeatureIO.pm#SUPPORTED_FORMATS >> >> >> Or should I stick to Fasta/GFF (or some other implementation)? >> >> Cheers, >> Dan. >> >> >> On 6 July 2010 15:50, Brian Osborne wrote: >>> Dan, >>> >>> There are 2 different directories for scripts, examples/ and scripts/. The examples/ directory accepts any sort of script. The scripts/ directory scripts can be installed when Bioperl is installed, if the user wishes. The guidelines are that scripts/ directory scripts should accept command-line arguments (which yours does), should be named with the suffix 'PLS', and should have POD documentation. So, all you need is some POD. Here's some example POD: >>> >>> =head1 NAME >>> >>> bioflat_index.pl - index sequence files using Bio::DB::Flat >>> >>> =head1 DESCRIPTION >>> >>> Create or update a biological sequence database indexed with the >>> Bio::DB::Flat indexing scheme. ?The arguments are a list of flat files >>> containing the sequence information to be indexed. >>> >>> =head1 USAGE >>> >>> bioflat_index.pl file1 file2 file3... >>> >>> Options: >>> >>> ? --create ? ? ? ? ? ? ?Create or reinitialize the index. ?If not specified, >>> ? ? ? ? ? ? ? ? ? ? ? ? the index must already exist. >>> >>> ? --format ? ? The format of the sequence files. ?Must be one >>> ? ? ? ? ? ? ? ? ? ? ? ? of "genbank", "swissprot", "embl" or "fasta". >>> >>> ? --location ? ? Path to the directory in which the index files >>> ? ? ? ? ? ? ? ? ? ? ? ? are stored. >>> >>> ? --dbname ? ? ? The symbolic name of the database to be created. >>> >>> ? --indextype ? ?Type of index to create. ?Either "bdb" or "flat". >>> ? ? ? ? ? ? ? ? ? ? ? ? "binarysearch" is the same as "flat". >>> >>> Options can be abbreviated. ?For example, use -i for --indextype. >>> >>> The following environment variables will be used as defaults if the >>> corresponding options are not provided: >>> >>> ? OBDA_FORMAT ? ? ?format of sequence file >>> ? OBDA_LOCATION ? ?path to directory in which index files are stored >>> ? OBDA_DBNAME ? ? ?name of database >>> ? OBDA_INDEX ? ? ? type of index to create >>> >>> =cut >>> >>> >>> On Jul 6, 2010, at 2:37 PM, Dan Bolser wrote: >>> >>>> Hello, >>>> >>>> I'd like to submit a script, 'bp_repeat_mask_sequence.pl'(?), to the >>>> set of scripts in BioPerl. Below is what I have so far. The script >>>> works by reading in a GFF of 'repeat_region's and a fasta file of >>>> sequences. It outputs a fasta sequence file with the repeats replaced >>>> by Xs. >>>> >>>> The script clearly needs to be more configurable, but I thought I'd >>>> send it along now to see if I'm working along the right lines, or if I >>>> should be using a different approach. >>>> >>>> Comments? >>>> >>>> >>>> Cheers, >>>> Dan. >>>> >>>> >>>> >>>> #!/usr/bin/perl -w >>>> >>>> use strict; >>>> use Getopt::Long; >>>> >>>> use Bio::SeqIO; >>>> use Bio::FeatureIO; >>>> >>>> >>>> >>>> ## Set options >>>> >>>> my $verbose = 0; >>>> my $seq_file; >>>> my $gff_file; >>>> >>>> GetOptions >>>> ( >>>> "verbose" => \$verbose, >>>> "seq=s" => \$seq_file, >>>> "gff=s" => \$gff_file, >>>> ) >>>> or die "failed to parse command line options\n"; >>>> >>>> die "fail $gff_file : $!\n" >>>> unless -s $gff_file; >>>> >>>> >>>> >>>> ## Set up the BioPerl objects >>>> >>>> my $seq_reader = >>>> Bio::SeqIO->new( -file => $seq_file, >>>> ? ? ? ? ? ? ? ?-format => 'fasta' >>>> ? ? ? ? ? ? ?); >>>> >>>> my $seq_writer = >>>> Bio::SeqIO->new( -fh => \*STDOUT, >>>> ? ? ? ? ? ? ? ?-format => 'fasta', >>>> ? ? ? ? ? ? ? ?-width => 80 >>>> ? ? ? ? ? ? ?); >>>> >>>> my $gff_reader = >>>> Bio::FeatureIO->new( -file => $gff_file, >>>> ? ? ? ? ? ? ? ? ? ?-format => 'GFF', >>>> ? ? ? ? ? ? ? ? ?); >>>> >>>> #warn $seq_reader->width, "\n"; exit; >>>> >>>> >>>> >>>> ## Run >>>> >>>> my (%repeats, $c); >>>> >>>> while ( my $feature = $gff_reader->next_feature() ) { >>>> if($verbose>1){ >>>> ?print >>>> ? ?join("\t", #$feature, >>>> ? ? ? ?$feature->seq_id, >>>> ? ? ? ?$feature->type->name, >>>> ? ? ? ?$feature->start, >>>> ? ? ? ?$feature->end, >>>> ? ? ? ), "\n"; >>>> } >>>> >>>> if($feature->type->name eq 'repeat_region'){ >>>> ?$c++; >>>> ?push @{$repeats{ $feature->seq_id }}, >>>> ? ?[$feature->start, >>>> ? ? $feature->end]; >>>> } >>>> >>>> # Debugging >>>> #last if $c > 100; >>>> } >>>> >>>> warn "read $c repeat_region features for ", >>>> scalar keys(%repeats), " sequences\n"; >>>> >>>> >>>> >>>> ## >>>> >>>> while(my $seq = $seq_reader->next_seq){ >>>> my $id = $seq->id; >>>> my $sequence = $seq->seq; >>>> >>>> print $id, "\n" >>>> ?if $verbose > 0; >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> for my $region (@{$repeats{ $id }}){ >>>> ?my ($start, $end) = @$region; >>>> ?print "$start\t$end\n" >>>> ? ?if $verbose > 1; >>>> >>>> ?substr($sequence, $start, $end - $start, 'X' x ($end - $start)); >>>> } >>>> >>>> print length($sequence), "\n" >>>> ?if $verbose > 0; >>>> >>>> $seq->seq($sequence); >>>> >>>> $seq_writer->write_seq($seq); >>>> >>>> # Debugging; >>>> #last; >>>> } >>>> >>>> warn "OK\n"; >>>> _______________________________________________ >>>> 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 Jul 12 12:42:58 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jul 2010 13:42:58 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" Message-ID: Seems I still can't log bugs here: https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 Error: Artifact: Only Artifact Admins Can Modify Private ArtifactTypes Here I my bug report: I'm following the tutorial here: http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html I successfully set up and browsed the first database (going no further than #data_file). I decided to try switching from an in memory (file-based) database to a DBI::mysql database. After taking the appropriate steps (see below), I get the following error when viewing the database in GB: The landmark named ctgA is not recognized. See the help pages for suggestions. I'm not sure why the landmark is found using a memory (file-based) database, but not found when using the same GFF loaded into mysql. This is the latest bioperl-live (although I'm still struggling with git). Any hints on what might be going wrong? I've a feeling I should perhaps roll back a few versions, as I noticed some SQL errors coming from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". Cheers, Dan. 1) I loaded the GFF: bp_seqfeature_load.pl -v -v -f -c -z \ --dsn dbi:mysql:mydb:myhost \ --namespace volvox \ --summary \ -u me -p secret \ databases/volvox/volvox_remarks.gff3 2) I changed the volvox.conf file: #db_args = -adaptor memory # -dir '$HTDOCS/databases/volvox' db_args = -adaptor DBI::mysql -dsn mydb:myhost -namespace volvox -user me -pass secret From shalabh.sharma7 at gmail.com Mon Jul 12 14:56:56 2010 From: shalabh.sharma7 at gmail.com (shalabh sharma) Date: Mon, 12 Jul 2010 10:56:56 -0400 Subject: [Bioperl-l] Intergenic regions Message-ID: Hi All, I am trying to find intergenic regions/sequences in genomes. Is there any bioperl module for that ? or any other package/software available? I would really appreciate if anyone can help me out. Thanks Shalabh From awitney at sgul.ac.uk Mon Jul 12 15:37:05 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Mon, 12 Jul 2010 16:37:05 +0100 Subject: [Bioperl-l] Intergenic regions In-Reply-To: References: Message-ID: If the genomes are already annotated then I guess you could just the Bio::Seq modules to pull out the intergenic regions. If there is no annotation yet then you would need to run some kind of gene prediction software first eg Genescan, Glimmer (google will throw up several choices). cheers adam On 12 Jul 2010, at 15:56, shalabh sharma wrote: > Hi All, > I am trying to find intergenic regions/sequences in genomes. Is > there any bioperl module for that ? or any other package/software available? > > I would really appreciate if anyone can help me out. > > Thanks > Shalabh > _______________________________________________ > 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 Jul 12 16:56:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 12 Jul 2010 11:56:12 -0500 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: Message-ID: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Dan. Is this maybe something for the GBrowse list? (cc'ing there JIC) chris On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > --dsn dbi:mysql:mydb:myhost \ > --namespace volvox \ > --summary \ > -u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args = -adaptor memory > # -dir '$HTDOCS/databases/volvox' > > db_args = -adaptor DBI::mysql > -dsn mydb:myhost > -namespace volvox > -user me > -pass secret > _______________________________________________ > 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 Tue Jul 13 07:49:44 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 08:49:44 +0100 Subject: [Bioperl-l] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: Cheers Chris, Is there a known good version of "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? I believe that this is one of the more common databases, so I'm surprised to find it broken. What would be the git command to roll back to a stable BioPerl / GBrowse? Sorry for the basic questions, Dan. On 12 July 2010 17:56, Chris Fields wrote: > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From mark.alston at BBSRC.AC.UK Tue Jul 13 10:47:04 2010 From: mark.alston at BBSRC.AC.UK (mark alston (TGAC)) Date: Tue, 13 Jul 2010 11:47:04 +0100 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... Message-ID: Hi, BioPerl newbie question coming up... I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. Here's my script after days of effort (I joke not): ######################################################################### use Bio::DB::Taxonomy ; my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects foreach my $nodelet (@taxa) { print $nodelet->to_string() . "\t" ; } ######################################################################### This outputs: 131567 2 1224 1236 91347 543 413496 28141 290339 If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because 2 corresponds to: bacteria (superkingdom) 1224 corresponds to: proteobacteria (phylum) etc etc 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) But how can I get the things I've underlined out via BioPerl? Many thanks, Mark ################################################ Dr Mark Alston, Computer Biologist, The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK. tel +44 (0)1603 450910 e-mail mark.alston at bbsrc.ac.uk web http://www.tgac.bbsrc.ac.uk ################################################ From cjfields at illinois.edu Tue Jul 13 12:58:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jul 2010 07:58:41 -0500 Subject: [Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects... In-Reply-To: References: Message-ID: Change to the following: { print $nodelet->scientific_name() . "\t" ; } chris On Jul 13, 2010, at 5:47 AM, mark alston (TGAC) wrote: > Hi, > BioPerl newbie question coming up... > I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples. > Here's my script after days of effort (I joke not): > ######################################################################### > use Bio::DB::Taxonomy ; > my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez'); > > my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ; > my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ; > > my @taxa = $bugTree->get_nodes ; ### returns an array of Bio::Tree:NodeI objects > > foreach my $nodelet (@taxa) > { print $nodelet->to_string() . "\t" ; } > ######################################################################### > > This outputs: > 131567 2 1224 1236 91347 543 413496 28141 290339 > > If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because > 2 corresponds to: bacteria (superkingdom) > 1224 corresponds to: proteobacteria (phylum) > etc etc > 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species) > > > But how can I get the things I've underlined out via BioPerl? > Many thanks, > Mark > > ################################################ > Dr Mark Alston, > Computer Biologist, > The Genome Analysis Centre, > Norwich Research Park, > Colney Lane, Norwich, NR4 7UH, UK. > > tel +44 (0)1603 450910 > e-mail mark.alston at bbsrc.ac.uk > web http://www.tgac.bbsrc.ac.uk > ################################################ > > > _______________________________________________ > 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 Tue Jul 13 17:15:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 13 Jul 2010 18:15:02 +0100 Subject: [Bioperl-l] Coordinate converter? Message-ID: Hi, When one sequence exists in the context of another larger sequence (with a precise start, end and strand), what is the easiest way to convert coordinates between the two sequences? I'm guessing there is an object I can load with the appropriate information with a conversion method? However, I'm stuck for details. I have implemented sub-sequences as features, but I'm not sure what to do next. Thanks for any hints, Dan. irc://irc.freenode.net/#bioperl From armendarez77 at hotmail.com Tue Jul 13 18:00:27 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:00:27 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Message-ID: Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 From randalls at bioinfo.wsu.edu Tue Jul 13 18:43:35 2010 From: randalls at bioinfo.wsu.edu (randalls at bioinfo.wsu.edu) Date: Tue, 13 Jul 2010 11:43:35 -0700 (PDT) Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: Message-ID: <108709378.25.1279046615031.JavaMail.root@mail> One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Tue Jul 13 18:38:24 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 13 Jul 2010 11:38:24 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <1A4207F8295607498283FE9E93B775B406D676E9@EX02.asurite.ad.asu.edu> And a 64-bit OS and program to be able to utilize greater than 3GB of RAM. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of randalls at bioinfo.wsu.edu Sent: Tuesday, July 13, 2010 11:44 AM To: armendarez77 at hotmail.com Cc: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PI D28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/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 armendarez77 at hotmail.com Tue Jul 13 18:57:54 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Tue, 13 Jul 2010 11:57:54 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: That would be nice, but not possible right now :) > Date: Tue, 13 Jul 2010 11:43:35 -0700 > From: randalls at bioinfo.wsu.edu > To: armendarez77 at hotmail.com > CC: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation > > One suggestion is to use a computer with a lot more memory...... > > Randall Svancara > Systems Administrator/DBA/Developer > Main Bioinformatics Laboratory > > > > ----- Original Message ----- > From: armendarez77 at hotmail.com > To: bioperl-l at lists.open-bio.org > Sent: Tuesday, July 13, 2010 11:00:27 AM > Subject: [Bioperl-l] Muscle Alignment and Memory Allocation > > Hello, > > I need to align 20-30 large full genome sequences (150,000+ bp each), > but I run out of memory. I've tried using -maxmb at the command line and > as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either > using it wrong or it's not working. > > I've also tried aligning 2 sequences at a time and then aligning those > alignments using the -profile command, but it's still too much. > > Do you have any advice on how to do such alignments? My attempts are > below. > > Thank you, > > Veronica > > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB > > Alignment not completed, cannot save. > > > > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout > 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.74 MB > > Alignment not completed, cannot save. > > > Using Bio::Tools::Run::Alignment::Muscle and -maxmb > > SCRIPT: my $inputFile = $ARGV[0]; > my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); > > my $alnObj = $factory->align($inputFile); > my $output = "output.clw"; > my $clwOut = Bio::AlignIO->new(-format=>'clustalw', > -file=>">$output.clw"); $clwOut->write_aln($alnObj); > > OUTPUT: > > MUSCLE v3.6 by Robert C. Edgar > > http://www.drive5.com/muscle This software is donated to the public > domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. > > 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 > 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3210.9 MB > > Alignment not completed, cannot save. > > --------------------- WARNING --------------------- > MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in > 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] > > --------------------------------------------------- > > > > > > > _________________________________________________________________ The > New Busy is not the too busy. Combine all your e-mail accounts with > Hotmail. > http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 > _______________________________________________ Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From David.Messina at sbc.su.se Tue Jul 13 19:05:16 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jul 2010 15:05:16 -0400 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <108709378.25.1279046615031.JavaMail.root@mail> References: <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4B92E3EE-1001-44EE-8D78-B3B05E78A13E@sbc.su.se> I would contact the MUSCLE authors to see what they say, but like Randall said I would suspect that you won't be able to do such a large multiple alignment in 4GB of RAM. Dave From kai.blin at biotech.uni-tuebingen.de Tue Jul 13 18:42:58 2010 From: kai.blin at biotech.uni-tuebingen.de (Kai Blin) Date: Tue, 13 Jul 2010 20:42:58 +0200 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: Message-ID: <1279046578.2560.14.camel@gonzo.home.kblin.org> On Tue, 2010-07-13 at 11:00 -0700, armendarez77 at hotmail.com wrote: Hi Veronica, > I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. The fact that this also fails on the command line tells me that you're not running into a BioPerl problem. See my comments inline below: [...] > 00:00:01 105 MB(-37%) Iter 1 6.25% Align node > *** OUT OF MEMORY *** > Memory allocated so far 3211.48 MB ^^^^^^^^^^ [...] > Using -maxmb at the command line: > > $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 ^^^^^^^^^^^^ You're running out of memory at 3211.48 MB, but you're telling muscle it's fine to use 4000 MB. Maybe you might want to provide less memory to -maxmb ..... Cheers, Kai -- Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de Interfakult?res Institut f?r Mikrobiologie und Infektionsmedizin Abteilung Mikrobiologie/Biotechnologie Eberhard-Karls-Universit?t T?bingen Auf der Morgenstelle 28 Phone : ++49 7071 29-78841 D-72076 T?bingen Fax : ++49 7071 29-5979 Deutschland Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben From jason at bioperl.org Tue Jul 13 22:41:24 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:41:24 -0700 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: Message-ID: <4C3CEB94.300@bioperl.org> Bio::Coordinate::Pair? Dan Bolser wrote, On 7/13/10 10:15 AM: > Hi, > > When one sequence exists in the context of another larger sequence > (with a precise start, end and strand), what is the easiest way to > convert coordinates between the two sequences? > > I'm guessing there is an object I can load with the appropriate > information with a conversion method? However, I'm stuck for details. > > I have implemented sub-sequences as features, but I'm not sure what to do next. > > Thanks for any hints, > Dan. > > > irc://irc.freenode.net/#bioperl > _______________________________________________ > 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 Tue Jul 13 22:44:32 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:44:32 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: References: , <108709378.25.1279046615031.JavaMail.root@mail> Message-ID: <4C3CEC50.6010102@bioperl.org> Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: > That would be nice, but not possible right now :) > > > > >> Date: Tue, 13 Jul 2010 11:43:35 -0700 >> From: randalls at bioinfo.wsu.edu >> To: armendarez77 at hotmail.com >> CC: bioperl-l at lists.open-bio.org >> Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> One suggestion is to use a computer with a lot more memory...... >> >> Randall Svancara >> Systems Administrator/DBA/Developer >> Main Bioinformatics Laboratory >> >> >> >> ----- Original Message ----- >> From: armendarez77 at hotmail.com >> To: bioperl-l at lists.open-bio.org >> Sent: Tuesday, July 13, 2010 11:00:27 AM >> Subject: [Bioperl-l] Muscle Alignment and Memory Allocation >> >> Hello, >> >> I need to align 20-30 large full genome sequences (150,000+ bp each), >> but I run out of memory. I've tried using -maxmb at the command line and >> as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either >> using it wrong or it's not working. >> >> I've also tried aligning 2 sequences at a time and then aligning those >> alignments using the -profile command, but it's still too much. >> >> Do you have any advice on how to do such alignments? My attempts are >> below. >> >> Thank you, >> >> Veronica >> >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3211.48 MB >> >> Alignment not completed, cannot save. >> >> >> >> Using -maxmb at the command line: >> >> $ muscle -in 07-13-2010_fullGenomes.fasta -clwout >> 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.74 MB >> >> Alignment not completed, cannot save. >> >> >> Using Bio::Tools::Run::Alignment::Muscle and -maxmb >> >> SCRIPT: my $inputFile = $ARGV[0]; >> my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); >> >> my $alnObj = $factory->align($inputFile); >> my $output = "output.clw"; >> my $clwOut = Bio::AlignIO->new(-format=>'clustalw', >> -file=>">$output.clw"); $clwOut->write_aln($alnObj); >> >> OUTPUT: >> >> MUSCLE v3.6 by Robert C. Edgar >> >> http://www.drive5.com/muscle This software is donated to the public >> domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. >> >> 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 >> 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 >> 00:00:01 105 MB(-37%) Iter 1 6.25% Align node >> *** OUT OF MEMORY *** >> Memory allocated so far 3210.9 MB >> >> Alignment not completed, cannot save. >> >> --------------------- WARNING --------------------- >> MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in >> 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] >> >> --------------------------------------------------- >> >> >> >> >> >> >> _________________________________________________________________ The >> New Busy is not the too busy. Combine all your e-mail accounts with >> Hotmail. >> http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 >> _______________________________________________ Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _________________________________________________________________ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 > _______________________________________________ > 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 Tue Jul 13 22:48:20 2010 From: jason at bioperl.org (Jason Stajich) Date: Tue, 13 Jul 2010 15:48:20 -0700 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> Message-ID: <4C3CED34.9050607@bioperl.org> Dan - I'm not convinced that contig:example is proper type/source for the landmarks & scaffold - i use 'scaffold:chromosome' in my data: What happens if you change the GFF3 file line from ctgA example contig 1 50000 . . . Name=ctgA to ctgA chromosome scaffold 1 50000 . . . Name=ctgA I think this can be tweaked in the config but there may be different defaults for the in memory and DBI::mysql implementation. -jason Dan Bolser wrote, On 7/13/10 12:49 AM: > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >>> Seems I still can't log bugs here: >>> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >>> >>> Error: >>> Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >>> >>> >>> Here I my bug report: >>> >>> I'm following the tutorial here: >>> >>> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >>> >>> >>> I successfully set up and browsed the first database (going no further >>> than #data_file). I decided to try switching from an in memory >>> (file-based) database to a DBI::mysql database. After taking the >>> appropriate steps (see below), I get the following error when viewing >>> the database in GB: >>> >>> The landmark named ctgA is not recognized. See the help pages >>> for suggestions. >>> >>> >>> I'm not sure why the landmark is found using a memory (file-based) >>> database, but not found when using the same GFF loaded into mysql. >>> >>> This is the latest bioperl-live (although I'm still struggling with git). >>> >>> Any hints on what might be going wrong? I've a feeling I should >>> perhaps roll back a few versions, as I noticed some SQL errors coming >>> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >>> >>> >>> Cheers, >>> Dan. >>> >>> >>> >>> 1) I loaded the GFF: >>> >>> bp_seqfeature_load.pl -v -v -f -c -z \ >>> --dsn dbi:mysql:mydb:myhost \ >>> --namespace volvox \ >>> --summary \ >>> -u me -p secret \ >>> databases/volvox/volvox_remarks.gff3 >>> >>> >>> 2) I changed the volvox.conf file: >>> >>> #db_args = -adaptor memory >>> # -dir '$HTDOCS/databases/volvox' >>> >>> db_args = -adaptor DBI::mysql >>> -dsn mydb:myhost >>> -namespace volvox >>> -user me >>> -pass secret >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 07:38:04 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 09:38:04 +0200 Subject: [Bioperl-l] getting only the aminoacids for a domain Message-ID: Hi, with these lines I download protein sequences matching "jjjj" uniprot code. !/usr/bin/perl use lib '/sw/share/bioperl-pm588'; use Bio::SeqIO; use Bio::DB::SwissProt; $db_obj = Bio::DB::SwissProt->new; $seq_obj = $db_obj->get_Seq_by_id('jjjj'); ...from here, I cut the sequences and get only a piece of each one (with subseq, between j1 and j2 residues) $shortened = $seq_obj->subseq(j1,j2); $seq_obj->seq($shortened); $seqio_obj = Bio::SeqIO->new(-file => '>jjjj.jletra.j1_j2.fasta', -format => 'fasta' ); $seqio_obj->write_seq($seq_obj); How can I download the sequence of ONLY THOSE AMINOACIDS that match, in uniprot, in the Sequence annotation section, Feature key: Domain & Description: lectin, ANK, Sushi,... the name of a given domain ? Is there any way of downloading all the existing fasta sequences for a given domain? Thanks in advance, JR From dan.bolser at gmail.com Wed Jul 14 10:27:02 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 11:27:02 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: <4C3CED34.9050607@bioperl.org> References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: Hi Jason, Thanks for the suggestion (see below). On 13 July 2010 23:48, Jason Stajich wrote: > Dan - > I'm not convinced that contig:example is proper type/source for the > landmarks & scaffold - i use 'scaffold:chromosome' in my data: > > What happens if you change the GFF3 file line from > ctgA example contig 1 50000 . . . Name=ctgA > to > ctgA chromosome scaffold 1 50000 . . . Name=ctgA > > > I think this can be tweaked in the config but there may be different > defaults for the in memory and DBI::mysql implementation. I found that this doesn't make any difference, however, I have found more information about what causes the bug. >From my previous email you see that I use bp_seqfeature_load.pl with the "--namespace volvox" option (I should have guessed it was something to do with this). Looking closely at the resulting tables I see that the following tables are empty volvox_attribute volvox_parent2child volvox_feature volvox_interval_stats volvox_name volvox_parent2child they are not empty when created without the "--namespace x" prefix, which is why DBI::mysql 'normally' works. All the other tables: volvox_attributelist volvox_locationlist volvox_meta volvox_sequence volvox_typelist appear to be created correctly, with or without the "--namespace x" prefix. Cheers, Dan. > -jason > Dan Bolser wrote, On 7/13/10 12:49 AM: > > Cheers Chris, > > Is there a known good version of > "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? > I believe that this is one of the more common databases, so I'm > surprised to find it broken. > > What would be the git command to roll back to a stable BioPerl / GBrowse? > > > Sorry for the basic questions, > Dan. > > On 12 July 2010 17:56, Chris Fields wrote: > > > Dan. > > Is this maybe something for the GBrowse list? (cc'ing there JIC) > > chris > > On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: > > > > Seems I still can't log bugs here: > https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 > > Error: > ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes > > > Here I my bug report: > > I'm following the tutorial here: > > http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html > > > I successfully set up and browsed the first database (going no further > than #data_file). I decided to try switching from an in memory > (file-based) database to a DBI::mysql database. After taking the > appropriate steps (see below), I get the following error when viewing > the database in GB: > > ? ? ? ?The landmark named ctgA is not recognized. See the help pages > for suggestions. > > > I'm not sure why the landmark is found using a memory (file-based) > database, but not found when using the same GFF loaded into mysql. > > This is the latest bioperl-live (although I'm still struggling with git). > > Any hints on what might be going wrong? I've a feeling I should > perhaps roll back a few versions, as I noticed some SQL errors coming > from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". > > > Cheers, > Dan. > > > > 1) I loaded the GFF: > > bp_seqfeature_load.pl -v -v -f -c -z \ > ?--dsn dbi:mysql:mydb:myhost \ > ?--namespace volvox \ > --summary \ > ?-u me -p secret \ > databases/volvox/volvox_remarks.gff3 > > > 2) I changed the volvox.conf file: > > #db_args ? ? ? = -adaptor memory > # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' > > db_args ? ? ? = -adaptor DBI::mysql > ? ? ? ? ? ? ? ?-dsn mydb:myhost > ? ? ? ? ? ? ? ?-namespace volvox > ? ? ? ? ? ? ? ?-user me > ? ? ? ? ? ? ? ?-pass secret > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > From joseramonblas at gmail.com Wed Jul 14 10:35:17 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 12:35:17 +0200 Subject: [Bioperl-l] install cpan on mac os x Message-ID: Hi, I have found several problems when installing CPAN in Mac OS X (version 10.6.4) previous to install Bioperl. What's the best choice for installing Bioperl on Mac OS X? I had it installed by using fink, but several modules are not found, I prefer a Unix installation. Is there any trick that I have to bear in mind? Thanks, JR From awitney at sgul.ac.uk Wed Jul 14 12:09:33 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 13:09:33 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: Message-ID: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> I have always found the CPAN route the best way of installing BioPerl on OSX. If you are having problems doing this then try posting any errors and someone may be able to help adam On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > Hi, > I have found several problems when installing CPAN in Mac OS X (version > 10.6.4) previous to install Bioperl. > > What's the best choice for installing Bioperl on Mac OS X? I had it > installed by using fink, but several modules are not found, I prefer a Unix > installation. Is there any trick that I have to bear in mind? > > Thanks, > > JR > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From joseramonblas at gmail.com Wed Jul 14 13:29:53 2010 From: joseramonblas at gmail.com (=?ISO-8859-1?Q?Jos=E9_Ram=F3n_Blas_Pastor?=) Date: Wed, 14 Jul 2010 15:29:53 +0200 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix When I do: >perl -MCPAN -e shell cpan> install Bundle::CPAN ...answer Yes to all... and the last lines of my installation are: t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 1. t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) Failed test: 1 Non-zero exit status: 255 Parse errors: Bad plan. You planned 255 tests but ran 2. Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) Result: FAIL Failed 67/85 test programs. 34/9260 subtests failed. make: *** [test_dynamic] Error 255 PMQS/IO-Compress-2.027.tar.gz /usr/bin/make test -- NOT OK //hint// to see the cpan-testers results for installing this module, try: reports PMQS/IO-Compress-2.027.tar.gz Running make install make test had returned bad status, won't install without force Failed during this command: ADAMK/File-HomeDir-0.91.tar.gz : make_test NO PMQS/IO-Compress-2.027.tar.gz : make_test NO ...any hint on where my failure comes from is appreciated. More info: Mac OS X 10.4 Xcode developer tools installed Thanks, JR El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on > OSX. > > If you are having problems doing this then try posting any errors and > someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a > Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Jul 14 13:36:45 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 14 Jul 2010 14:36:45 +0100 Subject: [Bioperl-l] install cpan on mac os x In-Reply-To: References: <544EFCA8-B460-425F-92FC-AD44EEA37E96@sgul.ac.uk> Message-ID: <74C17C09-7818-45C9-BD7C-896A74D37F17@sgul.ac.uk> looks like its failing to install PMQS/IO-Compress-2.027.tar.gz. Try installing it on its own cpan> install PMQS/IO-Compress-2.027.tar.gz On 14 Jul 2010, at 14:29, Jos? Ram?n Blas Pastor wrote: > I follow instructions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > > When I do: > >perl -MCPAN -e shell > cpan> install Bundle::CPAN > > ...answer Yes to all... and the last lines of my installation are: > > t/cz-06gzsetp.t (Wstat: 65280 Tests: 0 Failed: 0) > Non-zero exit status: 255 > Parse errors: No plan found in TAP output > t/cz-08encoding.t (Wstat: 65280 Tests: 1 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 29 tests but ran 1. > t/cz-14gzopen.t (Wstat: 65280 Tests: 2 Failed: 1) > Failed test: 1 > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 255 tests but ran 2. > Files=85, Tests=9260, 9 wallclock secs ( 1.09 usr 0.22 sys + 7.19 cusr 0.92 csys = 9.42 CPU) > Result: FAIL > Failed 67/85 test programs. 34/9260 subtests failed. > make: *** [test_dynamic] Error 255 > PMQS/IO-Compress-2.027.tar.gz > /usr/bin/make test -- NOT OK > //hint// to see the cpan-testers results for installing this module, try: > reports PMQS/IO-Compress-2.027.tar.gz > Running make install > make test had returned bad status, won't install without force > Failed during this command: > ADAMK/File-HomeDir-0.91.tar.gz : make_test NO > PMQS/IO-Compress-2.027.tar.gz : make_test NO > > ...any hint on where my failure comes from is appreciated. > > More info: > Mac OS X 10.4 > Xcode developer tools installed > > Thanks, > > JR > > El 14 de julio de 2010 14:09, Adam Witney escribi?: > > I have always found the CPAN route the best way of installing BioPerl on OSX. > > If you are having problems doing this then try posting any errors and someone may be able to help > > adam > > > On 14 Jul 2010, at 11:35, Jos? Ram?n Blas Pastor wrote: > > > Hi, > > I have found several problems when installing CPAN in Mac OS X (version > > 10.6.4) previous to install Bioperl. > > > > What's the best choice for installing Bioperl on Mac OS X? I had it > > installed by using fink, but several modules are not found, I prefer a Unix > > installation. Is there any trick that I have to bear in mind? > > > > Thanks, > > > > JR > > _______________________________________________ > > 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 Wed Jul 14 16:33:47 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 14 Jul 2010 17:33:47 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <4C3CEB94.300@bioperl.org> References: <4C3CEB94.300@bioperl.org> Message-ID: Brilliant! Thanks Jason. I found the example in the docs a bit confusing, so here is my version (hopefully to be built into an AGP object): #!/usr/bin/perl -w use Bio::Location::Simple; use Bio::Coordinate::Pair; my $ctg = Bio::Location::Simple-> new( -seq_id => 'ctg', -start => 1, -end => 999, -strand => +1 ); my $ctg_on_chr = Bio::Location::Simple-> new( -seq_id => 'chr', -start => 2001, -end => 2999, -strand => -1 ); my $agp = Bio::Coordinate::Pair-> new( -in => $ctg, -out => $ctg_on_chr ); my $match_on_ctg = Bio::Location::Simple-> new( -seq_id => 'hit', -start => 25, -end => 125, -strand => +1 ); print_loc( $agp->map( $match_on_ctg ) ); which gives: "chr 2875 2975 -1" I know the algorithm is simple, but it's not so simple to type it out, base perfect and bug free every time you need it. Cheers, Dan. On 13 July 2010 23:41, Jason Stajich wrote: > Bio::Coordinate::Pair? > > > Dan Bolser wrote, On 7/13/10 10:15 AM: >> >> Hi, >> >> When one sequence exists in the context of another larger sequence >> (with a precise start, end and strand), what is the easiest way to >> convert coordinates between the two sequences? >> >> I'm guessing there is an object I can load with the appropriate >> information with a conversion method? However, I'm stuck for details. >> >> I have implemented sub-sequences as features, but I'm not sure what to do >> next. >> >> Thanks for any hints, >> Dan. >> >> >> irc://irc.freenode.net/#bioperl >> _______________________________________________ >> 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 Jul 14 19:12:20 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jul 2010 13:12:20 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> Message-ID: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> On Jul 14, 2010, at 10:33, Dan Bolser wrote: > I found the example in the docs a bit confusing, Hey Dan, Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Dave From dan.bolser at gmail.com Thu Jul 15 08:42:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 09:42:12 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: On 14 July 2010 20:12, Dave Messina wrote: > > > > > On Jul 14, 2010, at 10:33, Dan Bolser wrote: > >> I found the example in the docs a bit confusing, > > > Hey Dan, > > Could you add your example to the wiki ( or modify the existing one to make it clearer ) ? It's not always clear to us when documentation is lacking, so it'd be great to capture your experience on this one. Sure thing Dave. The wiki is my preferred choice because it's easy for me to edit. However, having looked a git a bit, it seems like it should be easy for me to now mod the pod. I've put my code example with comments here: http://bioperl.org/wiki/Module:Bio::Coordinate::Pair One of the main reasons that I gave up editing the wiki is the very slow response time. I'm not sure what the bottleneck could be, but page loads, history checks, open for edits, and saves all take way longer than I'd like. This is especially frustrating when you want to make minor edits. (It may be worth noting that minor edits are the way wikis work [1]). This could be a good opportunity to spam the following conference: NETTAB 2010 - Workshop on biological wikis http://www.nettab.org/2010/ Thanks again for help, Dan. [1] http://www.parc.com/publication/1749/power-of-the-few-vs-wisdom-of-the-crowd.html > Dave > From David.Messina at sbc.su.se Thu Jul 15 14:59:43 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 15 Jul 2010 08:59:43 -0600 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> Message-ID: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> > I've put my code example with comments here: > > http://bioperl.org/wiki/Module:Bio::Coordinate::Pair Great, thanks. Much appreciated. > One of the main reasons that I gave up editing the wiki is the very > slow response time. Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > NETTAB 2010 - Workshop on biological wikis > http://www.nettab.org/2010/ Ah, Naples...love that city. If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. Dave From biopython at maubp.freeserve.co.uk Thu Jul 15 15:41:32 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 16:41:32 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Thu, Jul 15, 2010 at 3:59 PM, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. > BioPerl is a volunteer project and our hosting space is donated. > There were some zombie perl crontab processes were running - Mauricio has killed them and is looking at updating/fixing them. The wiki does seem faster now :) Peter From dan.bolser at gmail.com Thu Jul 15 17:46:45 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 15 Jul 2010 18:46:45 +0100 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On 15 July 2010 15:59, Dave Messina wrote: > >> I've put my code example with comments here: >> >> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair > > Great, thanks. Much appreciated. > > >> One of the main reasons that I gave up editing the wiki is the very >> slow response time. > > Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. How big is the wiki database? How about moving to http://bifx.org? >> NETTAB 2010 - Workshop on biological wikis >> http://www.nettab.org/2010/ > > Ah, Naples...love that city. > > If you see any other ways in which the BioPerl wiki can be improved, please contribute! Likewise, please let us know if you hear anything at the workshop relevant to BioPerl. > > > Dave From jovel_juan at hotmail.com Thu Jul 15 17:53:04 2010 From: jovel_juan at hotmail.com (Juan Jovel) Date: Thu, 15 Jul 2010 17:53:04 +0000 Subject: [Bioperl-l] How to convert SFF into Fastq Message-ID: Hello! How can I convert a SFF file from 454 into a Fastq format? Thanks a lot! JUAN _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline From biopython at maubp.freeserve.co.uk Thu Jul 15 18:40:05 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 15 Jul 2010 19:40:05 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: > > Hello! > > How can I convert a SFF file from 454 into a Fastq format? > > Thanks a lot! > > JUAN I am aware of three options, none of which use Perl, (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget which), to give you FASTA+QUAL, then using your tool of choice go to FASTQ (e.g. BioPerl). (2) Use the open source command line tool sff_extract (written in Python), it can do FASTA and QUAL, and I think there is an option for FASTQ too. http://bioinf.comav.upv.es/sff_extract/ (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. Things are more complex if you are working with paired end data... Peter From cjfields at illinois.edu Thu Jul 15 19:01:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:01:32 -0500 Subject: [Bioperl-l] Coordinate converter? In-Reply-To: References: <4C3CEB94.300@bioperl.org> <5BB307D6-6E42-469E-9998-F2EF2951F782@sbc.su.se> <32D4AE2D-C7F6-4F89-9E56-586CF743CB4B@sbc.su.se> Message-ID: On Jul 15, 2010, at 12:46 PM, Dan Bolser wrote: > On 15 July 2010 15:59, Dave Messina wrote: >> >>> I've put my code example with comments here: >>> >>> http://bioperl.org/wiki/Module:Bio::Coordinate::Pair >> >> Great, thanks. Much appreciated. >> >> >>> One of the main reasons that I gave up editing the wiki is the very >>> slow response time. >> >> Yep, absolutely. We're aware of it and are trying to work out a solution. BioPerl is a volunteer project and our hosting space is donated. > > How big is the wiki database? > > How about moving to http://bifx.org? Depends. We have talked about migrating most (all?) of the most significantly used parts (wiki, blogs) to other sources for a while. The GitHub move also played into that. But this would be a wider OBF-based issue, as it would also involve migrating other OBF-based wikis as well. chris From cjfields at illinois.edu Thu Jul 15 19:04:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 14:04:15 -0500 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: On Jul 15, 2010, at 1:40 PM, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter We are planning some tools for SFF work with BioPerl, possibly using BioLib's io_lib bindings. Much of this is to replace the legacy io_lib bindings from bioperl-ext, which is essentially dead at the moment. chris From armendarez77 at hotmail.com Thu Jul 15 19:20:43 2010 From: armendarez77 at hotmail.com (armendarez77 at hotmail.com) Date: Thu, 15 Jul 2010 12:20:43 -0700 Subject: [Bioperl-l] Muscle Alignment and Memory Allocation In-Reply-To: <4C3CEC50.6010102@bioperl.org> References: , <108709378.25.1279046615031.JavaMail.root@mail> , <4C3CEC50.6010102@bioperl.org> Message-ID: Thank you. I'll look into those programs. Veronica Date: Tue, 13 Jul 2010 15:44:32 -0700 From: jason at bioperl.org To: armendarez77 at hotmail.com CC: randalls at bioinfo.wsu.edu; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation Veronica - I think whole genome alignment is better applied with a program other than MUSCLE - or other than a typical MSA approach. See the extensive literature for this type of approach such as LAGAN, PECAN, MAVID, MAUVE, and MERCATOR (scaffold then align with MAVID or other tools) to name a few. If you insist on a traditional multiple sequence alignment only approach you may want to also try MAFFT but that is more suited for lots of sequences rather than long whole genome sequences. -jason armendarez77 at hotmail.com wrote, On 7/13/10 11:57 AM: That would be nice, but not possible right now :) Date: Tue, 13 Jul 2010 11:43:35 -0700 From: randalls at bioinfo.wsu.edu To: armendarez77 at hotmail.com CC: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation One suggestion is to use a computer with a lot more memory...... Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory ----- Original Message ----- From: armendarez77 at hotmail.com To: bioperl-l at lists.open-bio.org Sent: Tuesday, July 13, 2010 11:00:27 AM Subject: [Bioperl-l] Muscle Alignment and Memory Allocation Hello, I need to align 20-30 large full genome sequences (150,000+ bp each), but I run out of memory. I've tried using -maxmb at the command line and as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either using it wrong or it's not working. I've also tried aligning 2 sequences at a time and then aligning those alignments using the -profile command, but it's still too much. Do you have any advice on how to do such alignments? My attempts are below. Thank you, Veronica MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3211.48 MB Alignment not completed, cannot save. Using -maxmb at the command line: $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000 MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.74 MB Alignment not completed, cannot save. Using Bio::Tools::Run::Alignment::Muscle and -maxmb SCRIPT: my $inputFile = $ARGV[0]; my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000); my $alnObj = $factory->align($inputFile); my $output = "output.clw"; my $clwOut = Bio::AlignIO->new(-format=>'clustalw', -file=>">$output.clw"); $clwOut->write_aln($alnObj); OUTPUT: MUSCLE v3.6 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. 07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1 00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2 00:00:01 105 MB(-37%) Iter 1 6.25% Align node *** OUT OF MEMORY *** Memory allocated so far 3210.9 MB Alignment not completed, cannot save. --------------------- WARNING --------------------- MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in 07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA] --------------------------------------------------- _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 From cjfields at illinois.edu Fri Jul 16 04:38:10 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jul 2010 23:38:10 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release Message-ID: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> All, After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? chris From dan.bolser at gmail.com Fri Jul 16 07:59:01 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 16 Jul 2010 08:59:01 +0100 Subject: [Bioperl-l] How to convert SFF into Fastq In-Reply-To: References: Message-ID: (In theory,) the list of tools that produce and consume SFF can be found here: http://seqwiki.org/SFF Currently listed (and not already mentioned) is: * http://seqwiki.org/PyroBayes On 15 July 2010 19:40, Peter wrote: > On Thu, Jul 15, 2010 at 6:53 PM, Juan Jovel wrote: >> >> Hello! >> >> How can I convert a SFF file from 454 into a Fastq format? >> >> Thanks a lot! >> >> JUAN > > I am aware of three options, none of which use Perl, > > (1) Use the Roche (linux only) SFF tools (sffinfo or sfffile, I forget > which), to give you FASTA+QUAL, then using your tool of choice go to > FASTQ (e.g. BioPerl). > > (2) Use the open source command line tool sff_extract (written in Python), > it can do FASTA and QUAL, and I think there is an option for FASTQ too. > http://bioinf.comav.upv.es/sff_extract/ > > (3) Use Biopython's SeqIO, e.g. the Bio.SeqIO.convert() function. > > Things are more complex if you are working with paired end data... > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From chiragmatkarbioinfo at gmail.com Fri Jul 16 15:15:09 2010 From: chiragmatkarbioinfo at gmail.com (chirag matkar) Date: Fri, 16 Jul 2010 20:45:09 +0530 Subject: [Bioperl-l] Perl Web Crawling Message-ID: Hello, My Question Is not based on any Biological Application but in General How can we use Perl extensively in Web Crawling ? -- Regards, Chirag Matkar BTech Bioinformatics From cjfields at illinois.edu Fri Jul 16 15:23:01 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jul 2010 10:23:01 -0500 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <1E0BBB82-C6B4-4351-9133-7E8C4832D252@illinois.edu> http://lmgtfy.com/?q=Perl+Web+crawling chris On Jul 16, 2010, at 10:15 AM, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > > -- > Regards, > Chirag Matkar > BTech Bioinformatics > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From rmb32 at cornell.edu Fri Jul 16 15:23:04 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:04 -0700 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C407958.3010405@cornell.edu> Hi Chirag, This is off-topic for this list, it's not for general Perl questions. Search the CPAN at http://search.cpan.org, there are many modules there that can help you with this. In particular, I would look at WWW::Mechanize. Rob chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From rmb32 at cornell.edu Fri Jul 16 15:23:53 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Fri, 16 Jul 2010 08:23:53 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: <4C407989.5040609@cornell.edu> My thoughts on this: It sounds like a good plan. Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. So, something to think about going forward. Rob Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. That will be followed by releases of the run, db, and network distributions. Any other thoughts? Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From roy.chaudhuri at gmail.com Fri Jul 16 15:24:44 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Fri, 16 Jul 2010 16:24:44 +0100 Subject: [Bioperl-l] Perl Web Crawling In-Reply-To: References: Message-ID: <4C4079BC.5010601@gmail.com> Hi Chirag, This is not an appropriate mailing list for your question, it is intended for discussion of the BioPerl toolkit, not generic bioinformatics or Perl questions. Also, before sending a question to any mailing list you should attempt to answer it yourself. Did you try typing "Perl Web Crawling" into Google? The top few hits look like they may be useful. Cheers, Roy. On 16/07/2010 16:15, chirag matkar wrote: > Hello, > My Question Is not based on any Biological Application but in General > How can we use Perl extensively in Web Crawling ? > From jun.yin at ucd.ie Fri Jul 16 15:54:36 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Fri, 16 Jul 2010 16:54:36 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign Message-ID: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Dear all, I am the Google Summer of Code student working on refactoring Bio::Align subsystems. The first aim of the project is to recode Bio::SimpleAlign. This is because this package is really useful, but it was created a long time ago, written by several people, and a bit inconsistent mainly due to the above two reasons. I tried to keep the package consistent (e.g. method calling, coding styles) with the previous distribution. However, there are still a few changes. Since this package is created and used by the community, I think it is better to show it to everyone before it is merged with the major distribution. Any suggestions and criticisms are welcome. Here are the major improvements on Bio::SimpleAlign 1. MSA modifying and selection methods are more consistent and easier to use. I have enabled multiple/reverse selections for all sequences/columns selection methods, and change the names to be more understandable. For example, $aln->select() and $aln->select_noncont() are both deprecated, and renamed as $aln->select_Seqs() now. Because selections should be both in seqs and columns, which need to be explicit in the method call. For example, multiple sequence selections can be called by: $newaln=$aln->select_Seqs([4..10,20..35,37]); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37]); Or you can toggle selection(reverse selection) using: $newaln=$aln->select_Seqs([4..10,20..35,37],1); $newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37],-toggle=>1); If you can the method using the old ways, e.g. $newaln=$aln->select(1,5); A warning will be shown: select - deprecated method. Use select_Seqs() instead. And, the calling will be redirected to $newaln=$aln->select_Seqs([1..5]); 2. gap chars/missing chars are more consistent in the package Default values for gap char and missing char are now set in the package. Calling/Setting gap char should be made by calling $aln->gap_char("-"). 3. Some redundant methods are removed. The methods are moved to more reasonable categories. For example, $aln->select and $aln->select_noncont are deprecated now. Please use $aln->select_Seqs. 4. Some methods are renamed. Methods selecting/giving objects are capitalized, e.g. each_seq to each_Seq. Another example, the method is renamed to give a clearer information. $aln->purge is renamed into $aln->remove_redundant_Seqs $aln->splice_by_seq_pos is renamed to $aln->remove_gaps For further information, you can visit: http://spreadsheets.google.com/ccc?key=0AssLTcJFJMbXdDFfZGpJZlhidFY5blBneGdh QUZ6WFE &hl=en&authkey=CJTCw4QL Cheers, Jun Yin Ph.D. student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin From dan.bolser at gmail.com Fri Jul 16 23:15:03 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 17 Jul 2010 00:15:03 +0100 Subject: [Bioperl-l] [Gmod-gbrowse] Difference between "-adaptor memory" and "-adaptor DBI::mysql" In-Reply-To: References: <9A4C333F-8D07-4B47-9606-B529EFA864A0@illinois.edu> <4C3CED34.9050607@bioperl.org> Message-ID: On 14 July 2010 11:27, Dan Bolser wrote: > Hi Jason, > > Thanks for the suggestion (see below). > > On 13 July 2010 23:48, Jason Stajich wrote: >> Dan - >> I'm not convinced that contig:example is proper type/source for the >> landmarks & scaffold - i use 'scaffold:chromosome' in my data: >> >> What happens if you change the GFF3 file line from >> ctgA example contig 1 50000 . . . Name=ctgA >> to >> ctgA chromosome scaffold 1 50000 . . . Name=ctgA >> >> >> I think this can be tweaked in the config but there may be different >> defaults for the in memory and DBI::mysql implementation. > > I found that this doesn't make any difference, however, I have found > more information about what causes the bug. > > From my previous email you see that I use bp_seqfeature_load.pl with > the "--namespace volvox" option (I should have guessed it was > something to do with this). Looking closely at the resulting tables I > see that the following tables are empty > > volvox_attribute > volvox_parent2child > volvox_feature > volvox_interval_stats > volvox_name > volvox_parent2child > > > they are not empty when created without the "--namespace x" prefix, > which is why DBI::mysql 'normally' works. > > All the other tables: > > volvox_attributelist > volvox_locationlist > volvox_meta > volvox_sequence > volvox_typelist > > > appear to be created correctly, with or without the "--namespace x" prefix. It might be worth mentioning that this issue can be 'resolved' by not using the -f (fast load) option. i.e. its the specific combination of --namespace and -f that causes the bug. http://bugzilla.open-bio.org/show_bug.cgi?id=3110 > Cheers, > Dan. > >> -jason >> Dan Bolser wrote, On 7/13/10 12:49 AM: >> >> Cheers Chris, >> >> Is there a known good version of >> "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm" that I can roll back to? >> I believe that this is one of the more common databases, so I'm >> surprised to find it broken. >> >> What would be the git command to roll back to a stable BioPerl / GBrowse? >> >> >> Sorry for the basic questions, >> Dan. >> >> On 12 July 2010 17:56, Chris Fields wrote: >> >> >> Dan. >> >> Is this maybe something for the GBrowse list? (cc'ing there JIC) >> >> chris >> >> On Jul 12, 2010, at 7:42 AM, Dan Bolser wrote: >> >> >> >> Seems I still can't log bugs here: >> https://sourceforge.net/tracker/?func=add&group_id=27707&atid=511474 >> >> Error: >> ? ? ? ?Artifact: Only Artifact Admins Can Modify Private ArtifactTypes >> >> >> Here I my bug report: >> >> I'm following the tutorial here: >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/htdocs/tutorial/tutorial.html >> >> >> I successfully set up and browsed the first database (going no further >> than #data_file). I decided to try switching from an in memory >> (file-based) database to a DBI::mysql database. After taking the >> appropriate steps (see below), I get the following error when viewing >> the database in GB: >> >> ? ? ? ?The landmark named ctgA is not recognized. See the help pages >> for suggestions. >> >> >> I'm not sure why the landmark is found using a memory (file-based) >> database, but not found when using the same GFF loaded into mysql. >> >> This is the latest bioperl-live (although I'm still struggling with git). >> >> Any hints on what might be going wrong? I've a feeling I should >> perhaps roll back a few versions, as I noticed some SQL errors coming >> from "perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm". >> >> >> Cheers, >> Dan. >> >> >> >> 1) I loaded the GFF: >> >> bp_seqfeature_load.pl -v -v -f -c -z \ >> ?--dsn dbi:mysql:mydb:myhost \ >> ?--namespace volvox \ >> --summary \ >> ?-u me -p secret \ >> databases/volvox/volvox_remarks.gff3 >> >> >> 2) I changed the volvox.conf file: >> >> #db_args ? ? ? = -adaptor memory >> # ? ? ? ? ? ? ? -dir '$HTDOCS/databases/volvox' >> >> db_args ? ? ? = -adaptor DBI::mysql >> ? ? ? ? ? ? ? ?-dsn mydb:myhost >> ? ? ? ? ? ? ? ?-namespace volvox >> ? ? ? ? ? ? ? ?-user me >> ? ? ? ? ? ? ? ?-pass secret >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > From bernd.web at gmail.com Sat Jul 17 12:21:46 2010 From: bernd.web at gmail.com (Bernd Web) Date: Sat, 17 Jul 2010 14:21:46 +0200 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: Dear Jun, Thanks for your work on this. Just a few remarks. -is changing methods names indeed needed? this will break existing code (for some time) -i am not sure how naming is generally done now in BioPerl, but is used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has an "_" followed by a capital. I'd stick with each_seq like names. You now changed it too "each_Seq" but gap_char for example remained gap_char. But surely others know better how/if to change naming. > 2. gap chars/missing chars are more consistent in the package > Default values for gap char and missing char are now set in the package. > Calling/Setting gap char should be made by calling $aln->gap_char("-"). So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char. > Another example, the method is renamed to give a clearer information. > > $aln->purge is renamed into $aln->remove_redundant_Seqs Purge to me is a clear name in aln context ;-) > $aln->splice_by_seq_pos is renamed to $aln->remove_gaps But there was already a remove_gaps method. $aln2 = $aln->remove_gaps Function : Creates an aligment with gaps removed Title : splice_by_seq_pos Usage : $status = splice_by_seq_pos(1); Function: splices all aligned sequences where the specified sequence has gaps. So remove_gaps now takes an optional argument to indicate a 'reference' sequence for splicing? Cheers, Bernd From cjfields at illinois.edu Sat Jul 17 17:07:50 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 12:07:50 -0500 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: On Jul 17, 2010, at 7:21 AM, Bernd Web wrote: > Dear Jun, > > Thanks for your work on this. > Just a few remarks. > -is changing methods names indeed needed? this will break existing > code (for some time) There is expected to be a standard deprecation cycle along with this. Changes would not be merged in until after the 1.6.2 release. > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq", the new SimpleAlign now has > an "_" followed by a capital. I'd stick with each_seq like names. You > now changed it too "each_Seq" but gap_char for example remained > gap_char. But surely others know better how/if to change naming. Technically, we would like to standardize that when object(s) are returned (such as each_seq and it's previous incarnations) the method would have the class in caps, whereas simple data would not. There have been several starts along this path, but I think various methods (next_seq in SeqIO being one) still haven't changed. Also, just to point out, it's not terribly hard to alias these as needed: *eachSeq = \&each_Seq; >> 2. gap chars/missing chars are more consistent in the package >> Default values for gap char and missing char are now set in the package. >> Calling/Setting gap char should be made by calling $aln->gap_char("-"). > So the change here is that now the default values are actually set in > new, instead of setting a the default by calling gap_char. Maybe Jun could answer this, but to me this one makes sense (methods like this, which are relied upon for various reaons, need defaults for proper state). '-' is the most commonly-used symbol. >> Another example, the method is renamed to give a clearer information. >> >> $aln->purge is renamed into $aln->remove_redundant_Seqs > Purge to me is a clear name in aln context ;-) Possibly. However alignments can hold more than sequence data (stockholm format, for example), so maybe purge() on it's own is not descriptive enough. Jun, is remove_redundant_Seqs() an alias/reimplementation for purge()? The name might be a little misleading. >> $aln->splice_by_seq_pos is renamed to $aln->remove_gaps > But there was already a remove_gaps method. > $aln2 = $aln->remove_gaps > Function : Creates an aligment with gaps removed > > Title : splice_by_seq_pos > Usage : $status = splice_by_seq_pos(1); > Function: splices all aligned sequences where the specified sequence > has gaps. > > So remove_gaps now takes an optional argument to indicate a > 'reference' sequence for splicing? > > > Cheers, > Bernd This one I'm not sure about, as the two methods to me seem unrelated from name alone. Jun? chris From cjfields at illinois.edu Sun Jul 18 04:23:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jul 2010 23:23:49 -0500 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <4C407989.5040609@cornell.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> <4C407989.5040609@cornell.edu> Message-ID: On Jul 16, 2010, at 10:23 AM, Robert Buels wrote: > My thoughts on this: > > It sounds like a good plan. > > Also, it increases the urgency for the stuff on the development roadmap for the 1.7 release (well, releases!), the biggest of which is breaking things up into smaller distributions with independent versions. Precisely. > Jonathan Leto and I did some pilot work on the nuts and bolts of doing this, and we discovered something a bit counterintuitive: it's much better to do any large-scale splitting of BioPerl by starting at the root of the dependency graph, splitting off Bio::Root first. The reason for this is that each distribution's build system must keep a list of the modules that it depends on. > > If splitting is not done bottom-up, the dependency lists of dists that have already been split off have to be continually changed (manually, usually) to keep them up to date, which is not scalable for the large numbers of distributions that will be involved here. > > So, something to think about going forward. > > Rob I mentioned this at BOSC (it's briefly touched upon in the talk); it was agreed that the bottom-up approach is the best. Basically, if we can somehow emulate the larger distribution by allowing installation of the various packages then it makes life much easier for users, just have to decide what is the best approach. chris From rondonbio at yahoo.com.br Sun Jul 18 11:55:44 2010 From: rondonbio at yahoo.com.br (Rondon Neto) Date: Sun, 18 Jul 2010 04:55:44 -0700 (PDT) Subject: [Bioperl-l] Jaccard Dendrogram Message-ID: <750495.60162.qm@web63703.mail.re1.yahoo.com> Hi! Please, can I build a dendrogram from a jaccard distance matrix by Phylogenetic Analysis Pipeline? How to do that? Thank you Rondon From hlapp at drycafe.net Sun Jul 18 14:26:34 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 18 Jul 2010 10:26:34 -0400 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <89E90610-355B-4568-BFE2-301B7F4A7E61@drycafe.net> On Jul 17, 2010, at 8:21 AM, Bernd Web wrote: > -i am not sure how naming is generally done now in BioPerl, but is > used to be a like "eachSeq" or "each_seq" each_XXX is the old convention, which we aimed to deprecate before 1.4.x, in fact. Maybe we haven't swept through the entire codebase, but where we can we should certain change it. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From David.Messina at sbc.su.se Sun Jul 18 17:26:52 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 18 Jul 2010 11:26:52 -0600 Subject: [Bioperl-l] Jaccard Dendrogram In-Reply-To: <750495.60162.qm@web63703.mail.re1.yahoo.com> References: <750495.60162.qm@web63703.mail.re1.yahoo.com> Message-ID: Hi Rondon, No, I don't think BioPerl has the ability to do Jaccard distance calculations. Looks like SciPy-cluster can, though: http://code.google.com/p/scipy-cluster/ Also MATLAB probably. However, if you or anyone ese should be so inclined, it should be straightforward to adapt one of the existing BioPerl distance methods. See e.g. Bio::Align::DNAStatistics: http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html Dave On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > Hi! Please, can I build a dendrogram from a jaccard distance matrix by > Phylogenetic Analysis Pipeline? > How to do that? > > Thank you > > Rondon > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From florent.angly at gmail.com Mon Jul 19 08:47:39 2010 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 19 Jul 2010 18:47:39 +1000 Subject: [Bioperl-l] New Bio::Root::IO->_insert() method Message-ID: <4C44112B.1060701@gmail.com> Hi list, I needed a feature to insert text at an arbitrary line in a file for a Bioperl module I am working on. I coded it, called the new method _insert( ) and added it to the Bio::Root::IO module because I realized that it could be useful to other Bioperl modules. The method seems to be working well and does not cause tests to fail but let me know if you encounter issues with it. Regards, Florent From jun.yin at ucd.ie Mon Jul 19 10:43:50 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Mon, 19 Jul 2010 11:43:50 +0100 Subject: [Bioperl-l] Recoding Bio::SimpleAlign In-Reply-To: References: <001d01cb24ff$311e2270$935a6750$%yin@ucd.ie> Message-ID: <004c01cb272f$4626b880$d2742980$%yin@ucd.ie> Hi, Thx for all your comments. 1. About each_seq(each_Seq) As Chris Fields says, we tend to capitalize the method name which returns objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so it is better to use a capitalized name as each_Seq. But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because it may be confused with the each() function in Core. So it may need to be renamed to next_Seq eventually. Usually, what I do for the old method is: sub each_seq { my $self = shift; $self->deprecated("each_seq - deprecated method. Use each_Seq() instead."); $self->each_Seq(); } Thus, if you call the old method, it will still continue to run, but give a deprecated warning. This is done on all deprecated methods. 2. To Bernd Web, " So the change here is that now the default values are actually set in new, instead of setting a the default by calling gap_char." Yes, gap_char has a default value "-" now, so is missing_char "?" and match_char ".". 3. To Bernd Web and Chris Fields, remove_redundant_Seqs() is just an alias for purge(). However, splice_by_seq_pos() is reimplemented and merged with the old remove_gaps(), because these two methods are actually doing similar things. The new remove_gaps() is: Title : remove_gaps Usage : $aln2 = $aln->remove_gaps(-reference=>5) Function : Creates an aligment with gaps removed Returns : a Bio::SimpleAlign object Args : -GAPCHAR a gap character(optional) if none specified taken from $self->gap_char, -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) indicates that only all-gaps columns should be deleted -REFERENCE splices all aligned sequences where the specified sequence has gaps. If you call the old splice_by_seq_pos(), it will be redirected to remove_gaps() by: sub splice_by_seq_pos{ my $self = shift; $self->deprecated("splice_by_seq_pos - deprecated method. Use remove_gaps() instead."); $self->remove_gaps(-reference=>$_[0]); } When I finally finish the recoding for Bio::SimpleAlign, I will write an online HOWTO. Plus, I think I will include an update log, to show which method is renamed and which is reimplemented, thus to make things clearer. Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin __________ Information from ESET Smart Security, version of virus signature database 5291 (20100719) __________ The message was checked by ESET Smart Security. http://www.eset.com From kellert at ohsu.edu Mon Jul 19 17:05:24 2010 From: kellert at ohsu.edu (Tom Keller) Date: Mon, 19 Jul 2010 10:05:24 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 20 In-Reply-To: References: Message-ID: Greetings, R has a jaccard function also. See http://pbil.univ-lyon1.fr/library/prabclus/html/jaccard.html for a description. cheers, Thomas (Tom) Keller, PhD kellert at ohsu.edu 503.494.2442 6339b R Jones Hall (BSc/CROET) www.ohsu.edu/xd/research/research-cores/dna-analysis/ On Jul 19, 2010, at 9:00 AM, wrote: > Send Bioperl-l mailing list submissions to > bioperl-l at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/bioperl-l > or, via email, send a message with subject or body 'help' to > bioperl-l-request at lists.open-bio.org > > You can reach the person managing the list at > bioperl-l-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioperl-l digest..." > > > Today's Topics: > > 1. Re: Jaccard Dendrogram (Dave Messina) > 2. New Bio::Root::IO->_insert() method (Florent Angly) > 3. Re: Recoding Bio::SimpleAlign (Jun Yin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 18 Jul 2010 11:26:52 -0600 > From: Dave Messina > Subject: Re: [Bioperl-l] Jaccard Dendrogram > To: Rondon Neto > Cc: bioperl-l at lists.open-bio.org > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Hi Rondon, > > No, I don't think BioPerl has the ability to do Jaccard distance > calculations. Looks like SciPy-cluster can, though: > > http://code.google.com/p/scipy-cluster/ > > Also MATLAB probably. > > However, if you or anyone ese should be so inclined, it should be > straightforward to adapt one of the existing BioPerl distance methods. See > e.g. Bio::Align::DNAStatistics: > > http://doc.bioperl.org/bioperl-live/Bio/Align/DNAStatistics.html > > > > > Dave > > > > > > On Sun, Jul 18, 2010 at 05:55, Rondon Neto wrote: > >> Hi! Please, can I build a dendrogram from a jaccard distance matrix by >> Phylogenetic Analysis Pipeline? >> How to do that? >> >> Thank you >> >> Rondon >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > ------------------------------ > > Message: 2 > Date: Mon, 19 Jul 2010 18:47:39 +1000 > From: Florent Angly > Subject: [Bioperl-l] New Bio::Root::IO->_insert() method > To: bioperl-l BioPerl > Message-ID: <4C44112B.1060701 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi list, > I needed a feature to insert text at an arbitrary line in a file for a > Bioperl module I am working on. I coded it, called the new method > _insert( ) and added it to the Bio::Root::IO module because I realized > that it could be useful to other Bioperl modules. The method seems to be > working well and does not cause tests to fail but let me know if you > encounter issues with it. > Regards, > Florent > > > ------------------------------ > > Message: 3 > Date: Mon, 19 Jul 2010 11:43:50 +0100 > From: Jun Yin > Subject: Re: [Bioperl-l] Recoding Bio::SimpleAlign > To: "'Bernd Web'" > Cc: bioperl-l at lists.open-bio.org, 'Chris Fields' > , bernd.web at gmail.com > Message-ID: <004c01cb272f$4626b880$d2742980$%yin at ucd.ie> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > Thx for all your comments. > > 1. About each_seq(each_Seq) > As Chris Fields says, we tend to capitalize the method name which returns > objects. each_Seq actually returns a list of Bio::LocatableSeq objects, so > it is better to use a capitalized name as each_Seq. > But as Hilmar Lapp mentioned, each_XXX is not a clear name either, because > it may be confused with the each() function in Core. So it may need to be > renamed to next_Seq eventually. > > Usually, what I do for the old method is: > > sub each_seq { > my $self = shift; > $self->deprecated("each_seq - deprecated method. Use each_Seq() > instead."); > $self->each_Seq(); > } > > Thus, if you call the old method, it will still continue to run, but give a > deprecated warning. This is done on all deprecated methods. > > > 2. To Bernd Web, " So the change here is that now the default values are > actually set in new, instead of setting a the default by calling gap_char." > > Yes, gap_char has a default value "-" now, so is missing_char "?" and > match_char ".". > > 3. To Bernd Web and Chris Fields, > remove_redundant_Seqs() is just an alias for purge(). > However, splice_by_seq_pos() is reimplemented and merged with the old > remove_gaps(), because these two methods are actually doing similar things. > The new remove_gaps() is: > > Title : remove_gaps > Usage : $aln2 = $aln->remove_gaps(-reference=>5) > Function : Creates an aligment with gaps removed > Returns : a Bio::SimpleAlign object > Args : -GAPCHAR a gap character(optional) if none specified taken > from $self->gap_char, > -ALLGAPCOL $all_gaps_columns flag (1 or 0, default is 0) > indicates that only all-gaps columns should be deleted > -REFERENCE splices all aligned sequences where the specified > sequence has gaps. > > If you call the old splice_by_seq_pos(), it will be redirected to > remove_gaps() by: > sub splice_by_seq_pos{ > my $self = shift; > $self->deprecated("splice_by_seq_pos - deprecated method. Use > remove_gaps() instead."); > $self->remove_gaps(-reference=>$_[0]); > } > > When I finally finish the recoding for Bio::SimpleAlign, I will write an > online HOWTO. > Plus, I think I will include an update log, to show which method is renamed > and which is reimplemented, thus to make things clearer. > > Cheers, > Jun Yin > Ph.D.?student in U.C.D. > > Bioinformatics Laboratory > Conway Institute > University College Dublin > > > > __________ Information from ESET Smart Security, version of virus signature > database 5291 (20100719) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > > > > > > ------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > End of Bioperl-l Digest, Vol 87, Issue 20 > ***************************************** From jonathan at leto.net Mon Jul 19 22:59:27 2010 From: jonathan at leto.net (Jonathan Leto) Date: Mon, 19 Jul 2010 15:59:27 -0700 Subject: [Bioperl-l] Final BioPerl 1.6 release In-Reply-To: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> References: <095AF4D7-820D-4312-B927-0F4FC533DB9D@illinois.edu> Message-ID: Howdy, I recently found a bug in parsing InterPro XML, which I have created a bug for, as well as patches which fix the problem with a test case: http://bugzilla.open-bio.org/show_bug.cgi?id=3121 I would very much like to get feedback on this patch and have it included in the next 1.6.x release. Thanks, Duke On Thu, Jul 15, 2010 at 9:38 PM, Chris Fields wrote: > All, > > After a bit of discussion at BOSC and finding the code on trunk is in pretty decent shape (seems to be passing all tests for perl up to v5.12), I would like to go ahead and work towards another point release. ?This is likely the final point release in the 1.6.x series, barring any major bug fixes needed. > > I'll work towards syncing the 1.6 branch and pushing an initial alpha release early next week (1.6.1_1), followed by a few rounds prior to the final release. ?That will be followed by releases of the run, db, and network distributions. ?Any other thoughts? ?Suggestions? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Jonathan "Duke" Leto jonathan at leto.net http://leto.net From jay at jays.net Mon Jul 19 22:24:05 2010 From: jay at jays.net (Jay Hannah) Date: Mon, 19 Jul 2010 17:24:05 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <9331AD17-C3FB-47E9-80C3-2D1360E9EC8C@jays.net> Greetings, I opened bug 3120 today. Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? http://bugzilla.open-bio.org/show_bug.cgi?id=3120 http://bugzilla.open-bio.org/attachment.cgi?id=1526 Or maybe it's just me? :) Thanks, Jay Hannah http://biodoc.ist.unomaha.edu/wiki/User:Jhannah From ycchen1981 at gmail.com Tue Jul 20 03:47:45 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Tue, 20 Jul 2010 11:47:45 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.abi format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my $in = Bio::SeqIO->new(-file => "$inputfilename", -format => 'abi'); my $out = Bio::SeqIO->new(-file => ">$outputfilename", -format => 'phd'); while ( my $seq = $in->next_seq() ) { for my $curr(1 .. $seq->length()) { print "[",$seq->qualat($curr),"]:"; print "[",$seq->trace_index_at($curr),"]\t"; } $out->write_seq($seq); last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From Jonathan_Epstein at nih.gov Tue Jul 20 17:53:00 2010 From: Jonathan_Epstein at nih.gov (Jonathan Epstein) Date: Tue, 20 Jul 2010 13:53:00 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? Message-ID: <4C45E27C.9090400@nih.gov> Hi, I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. Then there's the small matter of loading the hg18 annotations into the appropriate relational database. Thanks in advance for your guidance, Jonathan From rmb32 at cornell.edu Tue Jul 20 18:42:36 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 20 Jul 2010 11:42:36 -0700 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <4C45EE1C.7080401@cornell.edu> Take a look at Bio::DB::SeqFeature::Store. It's got a loader that ships with bioperl, bp_seqfeature_load.pl. perldoc Bio::DB::SeqFeature::Store. From the sound of it, the GMOD/Chado stuff might be too heavyweight for what you are doing. But a good method for accessing a Chado schema from Perl is Bio::Chado::Schema, http://search.cpan.org/perldoc?Bio::Chado::Schema, which is based on DBIx::Class. Hope this helps! Rob Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features > associated with a particular genomic region in the hg18 human assembly. > This seems to require a relational database. Of course I would like to > do this using Bioperl. > > So then the question becomes: what's the best approach to use? > Biosql/BioPerl-db looks like the cleanest solution, but it's not clear > to me how up-to-date it is; it sort of looks like an abandoned project. > > CHADO/Gmod is more actively maintained, but I don't know how/whether I > can obtain BioPerl bindings. > > I am also open to using the UCSC databases as a starting point, since > I've already mirrored most of the human-related portions of the UCSC > environment. > > > Then there's the small matter of loading the hg18 annotations into the > appropriate relational database. > > > Thanks in advance for your guidance, > > Jonathan > > > > > > _______________________________________________ > 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 Jul 20 18:55:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jul 2010 13:55:15 -0500 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <827D02E9-9AA8-4474-BBA4-FC15BAAC49F4@illinois.edu> On Jul 20, 2010, at 12:53 PM, Jonathan Epstein wrote: > Hi, > > I need a reasonably rapid runtime method to extract the gene features associated with a particular genomic region in the hg18 human assembly. This seems to require a relational database. Of course I would like to do this using Bioperl. > > So then the question becomes: what's the best approach to use? Biosql/BioPerl-db looks like the cleanest solution, but it's not clear to me how up-to-date it is; it sort of looks like an abandoned project. Not really abandoned, but it won't help in this case unless you intend on converting to BioSQL. > CHADO/Gmod is more actively maintained, but I don't know how/whether I can obtain BioPerl bindings. Look at Bio::Schema:Chado. It's more middleware, no direct BioPerl bindings yet. > I am also open to using the UCSC databases as a starting point, since I've already mirrored most of the human-related portions of the UCSC environment. > > Then there's the small matter of loading the hg18 annotations into the appropriate relational database. > > Thanks in advance for your guidance, > > Jonathan Bio::DB::SeqFeature::Store. Export the data into GTF; I think the database will load this (via Bio::DB::SeqFeature::Store::GFF2Loader). Otherwise, using the ensembl perl API is an option. One can install the database locally and use the Ensembl Perl API to extract the information you need. There were modules that were intended as interfaces to the remote UCSC databases but (IIRC) there was significant concern from the UCSC folks about overloading the UCSC server with queries, so they were basically deprecated (were only partially developed anyway). chris From hlapp at drycafe.net Tue Jul 20 19:40:10 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Tue, 20 Jul 2010 15:40:10 -0400 Subject: [Bioperl-l] best method for dealing with hg18 seq-features in a relational database? In-Reply-To: <4C45E27C.9090400@nih.gov> References: <4C45E27C.9090400@nih.gov> Message-ID: <0369BC4D-9769-47AE-AF6C-B43BAAEC2327@drycafe.net> On Jul 20, 2010, at 1:53 PM, Jonathan Epstein wrote: > Biosql/BioPerl-db looks like the cleanest solution, but it's not > clear to me how up-to-date it is; it sort of looks like an abandoned > project. It's not abandoned at all. I'm not sure though it serves your use-case - it sounds like some GFF store would meet your needs much better. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From florent.angly at gmail.com Tue Jul 20 22:05:22 2010 From: florent.angly at gmail.com (Florent Angly) Date: Wed, 21 Jul 2010 08:05:22 +1000 Subject: [Bioperl-l] Fwd: gene extraction script Message-ID: <4C461DA2.5090009@gmail.com> -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ From awitney at sgul.ac.uk Wed Jul 21 08:02:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 09:02:01 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <84B8D550-E4CA-4027-99A8-D05F1B5E8DEE@sgul.ac.uk> Hi Nicholas, If you just want to retrieve sequences from GenBank, try this: http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl HTH adam On 20 Jul 2010, at 23:05, Florent Angly wrote: > > > -------- Original Message -------- > Subject: gene extraction script > Date: Tue, 20 Jul 2010 15:56:36 +0100 > From: Nicholas Brown > To: > > > > Hi, > > Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? > Thanks so much for your time in reading this. > > Kind Regards, > > Nicholas Brown > > Script > http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl > #!/usr/bin/perl -w > # $Id$ > =pod > > > =head1 NAME > > > extract_genes.pl - extract genomic sequences from NCBI files > using BioPerl > > > =head1 DESCRIPTION > > > This script is a simple solution to the problem of > extracting genomic regions corresponding to genes. There are other > solutions, this particular approach uses genomic sequence > files from NCBI and gene coordinates from Entrez Gene. > > > The first time this script is run it will be slow as it will > extract species-specific data from the gene2accession file and create > a storable hash (retrieving the positional data from this hash is > significantly faster than reading gene2accession each time the script > runs). The subsequent runs should be fast. > > > =head1 INSTALLATION > > > =head2 > > > Install BioPerl, full instructions at http://bioperl.org. > > > =head2 Download gene2accession.gz > > > Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into > your working directory and gunzip it. > > > =head2 Download sequence files > > > Create one or more species directories in the working directory, the > directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). > > > Download the nucleotide fasta files for a given species from its CHR* > directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a > species directory. The sequence files will have the suffix ".fna" or > "fa.gz", gunzip if necessary. > > > =head2 Determine Taxon id > > > Determine the taxon id for the given species. This id is the first column > in the gene2accession file. Modify the %species hash in this script > such that name of your species directory is a key and the taxon id is the > value. > > > =head2 Command-line options > > > -i Gene id > -s Name of species directory > -h Help > > > Example: > > > extract_genes.pl -i 850302 -s Sc > > > =cut > > > use strict; > use Bio::DB::Fasta; > use Getopt::Long; > use Storable; > > my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae > "Ec" => 83333, # Escherichia coli K12 > "Hs" => 9606 # H. sapiens > ); > > my ($help,$id,$name); > > GetOptions( "s=s" => \$name, > "i=i" => \$id, > "h" => \$help ); > > usage() if ($help || !$id || !$name); > > my $storedHash = $name . ".dump"; > > # create index for a directory of fasta files > my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); > > # extract species-specific data from gene2accession > unless (-e $storedHash) { > my $ref; > # extract species-specific information from gene2accession > open MYIN,"gene2accession" or die "No gene2accession file\n"; > while () { > my @arr = split "\t",$_; > if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { > ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, > $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = > ($arr[9], $arr[10], $arr[11], $arr[7]); > } > } > # save species-specific information using Storable > store $ref, $storedHash; > } > > # retrieve the species-specific data from a stored hash > my $ref = retrieve($storedHash); > > # retrieve sequence and sub-sequence > if (defined $ref->{$id}) { > my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); > my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); > $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); > > # Insert SeqIO options here... > print $seq->seq,"\n"; > } else { > print "Cannot find id: $id\n"; > } > > sub make_my_id { > my $line = shift; > $line =~ /ref\|([^|]+)/; > $1; > } > > sub usage { > system "perldoc $0"; > exit; > } > > __END__ > > > _______________________________________________ > 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 Jul 21 09:43:35 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 21 Jul 2010 10:43:35 +0100 Subject: [Bioperl-l] Fwd: Fwd: gene extraction script References: <4C46B84C.4000702@univ-montp2.fr> Message-ID: forwarding to the original poster and the list... Begin forwarded message: > From: Laurent MANCHON > Date: 21 July 2010 10:05:16 GMT+01:00 > To: Adam Witney > Subject: Re: [Bioperl-l] Fwd: gene extraction script > Reply-To: lmanchon at univ-montp2.fr > > another program you can use. > > > #!/usr/bin/perl > # retrieve sequences from genbank > # read list of GenBank access number from a file and write to output.txt file > > use LWP::UserAgent; > use Bio::SeqIO; > use Bio::DB::GenBank; > $cpt=0; > $outfile = "outfile.txt"; > chomp($outfile); > $gb = new Bio::DB::GenBank; > while (<>) { > ($Fld1) = split(' ', $_, 9999); > $out = Bio::SeqIO->new('-file' => ">>$outfile",'-format' => 'fasta'); > $acc = $Fld1; > $cpt++; > print $acc,"\t$cpt"," retrieved\n"; > $seqio = $gb->get_Stream_by_acc([$acc]); > while( $seq = $seqio->next_seq() ) { > open(LOG,">>$outfile"); > printf LOG '%s ', ">" . $acc; > $out->write_seq($seq); > close(LOG); > } > > > > > > Adam Witney a ?crit : >> >> Hi Nicholas, >> >> If you just want to retrieve sequences from GenBank, try this: >> >> http://github.com/bioperl/bioperl-live/blob/master/examples/db/getGenBank.pl >> >> HTH >> >> adam >> >> >> On 20 Jul 2010, at 23:05, Florent Angly wrote: >> >> >>> -------- Original Message -------- >>> Subject: gene extraction script >>> Date: Tue, 20 Jul 2010 15:56:36 +0100 >>> From: Nicholas Brown >>> To: >>> >>> >>> >>> Hi, >>> >>> Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? >>> Thanks so much for your time in reading this. >>> >>> Kind Regards, >>> >>> Nicholas Brown >>> >>> Script >>> http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_genes.pl >>> #!/usr/bin/perl -w >>> # $Id$ >>> =pod >>> >>> >>> =head1 NAME >>> >>> >>> extract_genes.pl - extract genomic sequences from NCBI files >>> using BioPerl >>> >>> >>> =head1 DESCRIPTION >>> >>> >>> This script is a simple solution to the problem of >>> extracting genomic regions corresponding to genes. There are other >>> solutions, this particular approach uses genomic sequence >>> files from NCBI and gene coordinates from Entrez Gene. >>> >>> >>> The first time this script is run it will be slow as it will >>> extract species-specific data from the gene2accession file and create >>> a storable hash (retrieving the positional data from this hash is >>> significantly faster than reading gene2accession each time the script >>> runs). The subsequent runs should be fast. >>> >>> >>> =head1 INSTALLATION >>> >>> >>> =head2 >>> >>> >>> Install BioPerl, full instructions at http://bioperl.org. >>> >>> >>> =head2 Download gene2accession.gz >>> >>> >>> Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into >>> your working directory and gunzip it. >>> >>> >>> =head2 Download sequence files >>> >>> >>> Create one or more species directories in the working directory, the >>> directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). >>> >>> >>> Download the nucleotide fasta files for a given species from its CHR* >>> directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a >>> species directory. The sequence files will have the suffix ".fna" or >>> "fa.gz", gunzip if necessary. >>> >>> >>> =head2 Determine Taxon id >>> >>> >>> Determine the taxon id for the given species. This id is the first column >>> in the gene2accession file. Modify the %species hash in this script >>> such that name of your species directory is a key and the taxon id is the >>> value. >>> >>> >>> =head2 Command-line options >>> >>> >>> -i Gene id >>> -s Name of species directory >>> -h Help >>> >>> >>> Example: >>> >>> >>> extract_genes.pl -i 850302 -s Sc >>> >>> >>> =cut >>> >>> >>> use strict; >>> use Bio::DB::Fasta; >>> use Getopt::Long; >>> use Storable; >>> >>> my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae >>> "Ec" => 83333, # Escherichia coli K12 >>> "Hs" => 9606 # H. sapiens >>> ); >>> >>> my ($help,$id,$name); >>> >>> GetOptions( "s=s" => \$name, >>> "i=i" => \$id, >>> "h" => \$help ); >>> >>> usage() if ($help || !$id || !$name); >>> >>> my $storedHash = $name . ".dump"; >>> >>> # create index for a directory of fasta files >>> my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); >>> >>> # extract species-specific data from gene2accession >>> unless (-e $storedHash) { >>> my $ref; >>> # extract species-specific information from gene2accession >>> open MYIN,"gene2accession" or die "No gene2accession file\n"; >>> while () { >>> my @arr = split "\t",$_; >>> if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { >>> ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, >>> $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = >>> ($arr[9], $arr[10], $arr[11], $arr[7]); >>> } >>> } >>> # save species-specific information using Storable >>> store $ref, $storedHash; >>> } >>> >>> # retrieve the species-specific data from a stored hash >>> my $ref = retrieve($storedHash); >>> >>> # retrieve sequence and sub-sequence >>> if (defined $ref->{$id}) { >>> my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); >>> my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); >>> $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); >>> >>> # Insert SeqIO options here... >>> print $seq->seq,"\n"; >>> } else { >>> print "Cannot find id: $id\n"; >>> } >>> >>> sub make_my_id { >>> my $line = shift; >>> $line =~ /ref\|([^|]+)/; >>> $1; >>> } >>> >>> sub usage { >>> system "perldoc $0"; >>> exit; >>> } >>> >>> __END__ >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 jun.yin at ucd.ie Wed Jul 21 10:32:25 2010 From: jun.yin at ucd.ie (Jun Yin) Date: Wed, 21 Jul 2010 11:32:25 +0100 Subject: [Bioperl-l] Fwd: gene extraction script In-Reply-To: <4C461DA2.5090009@gmail.com> References: <4C461DA2.5090009@gmail.com> Message-ID: <012201cb28c0$027eb000$077c1000$%yin@ucd.ie> Hi, Nicolas, You don't need to edit the original code. Usually the package developed by the community provides enough methods for you. You may consider to use the recent developed package Bio::DB::EUtilities to retrieve the sequences from GenBank. See HOWTO here: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook Cheers, Jun Yin Ph.D.?student in U.C.D. Bioinformatics Laboratory Conway Institute University College Dublin -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Florent Angly Sent: Tuesday, July 20, 2010 11:05 PM To: bioperl-l List; n.brown at nhm.ac.uk Subject: [Bioperl-l] Fwd: gene extraction script -------- Original Message -------- Subject: gene extraction script Date: Tue, 20 Jul 2010 15:56:36 +0100 From: Nicholas Brown To: Hi, Sorry to distrub, I'm currently working at the natural history museum on some DNA sequencing techniques and I came accross a script you posted ( see below) which I think maybe helpful. The problem I have is that I have lots of sequnces of the same Mitochondrial genomes of different species aligned and I would like to extract the genes from each of the sequences easily, I wondered if there was an easy modificaiton to your script that I could perform that would allow me to do this? The sequences for the genes are already submitted to genbank, so i was just wondering if this would be a quicker simplier way than doing it manually? Thanks so much for your time in reading this. Kind Regards, Nicholas Brown Script http://github.com/bioperl/bioperl-live/blob/master/examples/tools/extract_ge nes.pl #!/usr/bin/perl -w # $Id$ =pod =head1 NAME extract_genes.pl - extract genomic sequences from NCBI files using BioPerl =head1 DESCRIPTION This script is a simple solution to the problem of extracting genomic regions corresponding to genes. There are other solutions, this particular approach uses genomic sequence files from NCBI and gene coordinates from Entrez Gene. The first time this script is run it will be slow as it will extract species-specific data from the gene2accession file and create a storable hash (retrieving the positional data from this hash is significantly faster than reading gene2accession each time the script runs). The subsequent runs should be fast. =head1 INSTALLATION =head2 Install BioPerl, full instructions at http://bioperl.org. =head2 Download gene2accession.gz Download this file from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA into your working directory and gunzip it. =head2 Download sequence files Create one or more species directories in the working directory, the directory names do not have to match those at NCBI (e.g. "Sc", "Hs"). Download the nucleotide fasta files for a given species from its CHR* directories at ftp://ftp.ncbi.nlm.nih.gov/genomes and put these files into a species directory. The sequence files will have the suffix ".fna" or "fa.gz", gunzip if necessary. =head2 Determine Taxon id Determine the taxon id for the given species. This id is the first column in the gene2accession file. Modify the %species hash in this script such that name of your species directory is a key and the taxon id is the value. =head2 Command-line options -i Gene id -s Name of species directory -h Help Example: extract_genes.pl -i 850302 -s Sc =cut use strict; use Bio::DB::Fasta; use Getopt::Long; use Storable; my %species = ( "Sc" => 4932, # Saccharomyces cerevisiae "Ec" => 83333, # Escherichia coli K12 "Hs" => 9606 # H. sapiens ); my ($help,$id,$name); GetOptions( "s=s" => \$name, "i=i" => \$id, "h" => \$help ); usage() if ($help || !$id || !$name); my $storedHash = $name . ".dump"; # create index for a directory of fasta files my $db = Bio::DB::Fasta->new($name, -makeid => \&make_my_id); # extract species-specific data from gene2accession unless (-e $storedHash) { my $ref; # extract species-specific information from gene2accession open MYIN,"gene2accession" or die "No gene2accession file\n"; while () { my @arr = split "\t",$_; if ($arr[0] == $species{$name}&& $arr[9] =~ /\d+/&& $arr[10] =~ /\d+/) { ($ref->{$arr[1]}->{"start"}, $ref->{$arr[1]}->{"end"}, $ref->{$arr[1]}->{"strand"}, $ref->{$arr[1]}->{"id"}) = ($arr[9], $arr[10], $arr[11], $arr[7]); } } # save species-specific information using Storable store $ref, $storedHash; } # retrieve the species-specific data from a stored hash my $ref = retrieve($storedHash); # retrieve sequence and sub-sequence if (defined $ref->{$id}) { my $chr = $db->get_Seq_by_id($ref->{$id}->{"id"}); my $seq = $chr->trunc($ref->{$id}->{"start"},$ref->{$id}->{"end"}); $seq = $seq->revcom if ($ref->{$id}->{"strand"} eq "-"); # Insert SeqIO options here... print $seq->seq,"\n"; } else { print "Cannot find id: $id\n"; } sub make_my_id { my $line = shift; $line =~ /ref\|([^|]+)/; $1; } sub usage { system "perldoc $0"; exit; } __END__ _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5296 (20100720) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com __________ Information from ESET Smart Security, version of virus signature database 5297 (20100721) __________ The message was checked by ESET Smart Security. http://www.eset.com From amritavisdom at gmail.com Sat Jul 17 11:21:27 2010 From: amritavisdom at gmail.com (AMRITA VISDOM) Date: Sat, 17 Jul 2010 16:51:27 +0530 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita From ycchen1981 at gmail.com Mon Jul 19 07:11:39 2010 From: ycchen1981 at gmail.com (=?Big5?B?s6+r27z9?=) Date: Mon, 19 Jul 2010 15:11:39 +0800 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO Message-ID: Hi, I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, bioperl-ext-1.5.1, and io-lib-1.8.11; my OS was 32-bit, Centos 5.2. When I convert abi-format files to phd-format files, the value of quality of all bases are '0', and the value of trace_index of all bases are undefined. Is there any possible reason leading to this problem? Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is 0.980904.e in phd files; if this is the case, where can I find phred executers? The following is the code utilizing BioPerl and results from BioPerl and Phred respectively: ============================================== #!/usr/bin/perl -w unshift(@INC, "/opt/BioPerl-1.6.1/"); unshift(@INC, "/opt/bioperl-ext"); use strict; use Bio::SeqIO; my $inputfilename='./HMA040184H12.T3.ab1'; my $outputfilename='test11.phd'; my ?$in ?= Bio::SeqIO->new(-file => "$inputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'abi'); my ?$out = Bio::SeqIO->new(-file => ">$outputfilename", ? ? ? ? ? ? ? ? ? ? ? ?-format => 'phd'); while ( my $seq = $in->next_seq() ) { ? ? ? for my $curr(1 .. ?$seq->length()) { ? ? ? ? ? ? ? print "[",$seq->qualat($curr),"]:"; ? ? ? ? ? ? ? print "[",$seq->trace_index_at($curr),"]\t"; ? ? ? } ? ? ? $out->write_seq($seq); ? ? ? last; } ================== test11.phd (by Bio::SeqIO) ================= BEGIN_SEQUENCE (null) BEGIN_COMMENT CHROMAT_FILE: unknown ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Mon Jul 19 11:59:09 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown END_COMMENT BEGIN_DNA A 0 G 0 G 0 G 0 G 0 . . . . G 0 T 0 T 0 G 0 T 0 C 0 G 0 C 0 T 0 A 0 C 0 END_DNA END_SEQUENCE ================== .phd (by phred 0.020425.c) ======================= BEGIN_SEQUENCE HMA040184H12.T3.ab1 BEGIN_COMMENT CHROMAT_FILE: HMA040184H12.T3.ab1 ABI_THUMBPRINT: 0 PHRED_VERSION: 0.020425.c CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: Fri Jul 9 16:20:59 2010 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 11905 TRIM: 38 900 0.0500 TRACE_PEAK_AREA_RATIO: 0.0630 CHEM: term DYE: big END_COMMENT BEGIN_DNA a 11 2 g 11 13 g 11 22 a 11 37 a 11 52 g 8 65 c 6 76 t 6 91 c 6 97 . . . a 14 11840 c 16 11849 a 16 11861 a 12 11873 c 12 11885 g 12 11897 END_DNA END_SEQUENCE ================================================ Sincerely yours, Yen-Chang Chen From amritavisdom at gmail.com Mon Jul 19 11:25:19 2010 From: amritavisdom at gmail.com (Amritavisdom) Date: Mon, 19 Jul 2010 04:25:19 -0700 (PDT) Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl Message-ID: <29203643.post@talk.nabble.com> Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita -- View this message in context: http://old.nabble.com/Parsing-Alternative-Splicing-Gene-information-from-Genbank-file-using-Bioperl-tp29203643p29203643.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From gabriel.jabud at gmail.com Tue Jul 20 18:36:54 2010 From: gabriel.jabud at gmail.com (Gabriel Ab) Date: Tue, 20 Jul 2010 11:36:54 -0700 (PDT) Subject: [Bioperl-l] Finding mutations in Blast files Message-ID: <29216321.post@talk.nabble.com> I'm trying to write a script to find mutations in a Blast output file. The result should look something like [A/G] (query/subject) for SNPs and [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if possible. I was able to get both the query and subject sequence extracted from blast files, but parsing through that for mutations without the help of modules and writing them like above is harder than it sounds. Deletions and other things in the alignment can make it very tricky. I tried looking for modules that would make this task easier but I couldn't find anything. Can someone point me in the right direction on how to do this or let me know about modules that could help? Thanks. -- View this message in context: http://old.nabble.com/Finding-mutations-in-Blast-files-tp29216321p29216321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From taw-bioperl at dowfamily.net Tue Jul 20 23:46:05 2010 From: taw-bioperl at dowfamily.net (Ycart) Date: Tue, 20 Jul 2010 23:46:05 +0000 (UTC) Subject: [Bioperl-l] Accessing karyotype data from Ensembl Message-ID: Hi, I am trying to figure out the correct syntax to access the karyotype data from the Ensembl database. I need to use the start and end base pair coordinates for the karyotype bands in a separate program, which means I need to be able to use that data, not just view it. I'm thinking that it will be like getting slices as described in the Core API Tutorial, but with some other word than 'Slice' in: my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); Any ideas on how to do this under the current API? -Tracy From cjfields at illinois.edu Wed Jul 21 21:43:32 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 16:43:32 -0500 Subject: [Bioperl-l] Accessing karyotype data from Ensembl In-Reply-To: References: Message-ID: You should contact the ensembl mail list for ensembl-related questions; this lies outside the bioperl domain. chris On Jul 20, 2010, at 6:46 PM, Ycart wrote: > Hi, > > I am trying to figure out the correct syntax to access the karyotype data from > the Ensembl database. I need to use the start and end base pair coordinates for > the karyotype bands in a separate program, which means I need to be able to use > that data, not just view it. > > I'm thinking that it will be like getting slices as described in the Core API > Tutorial, but with some other word than 'Slice' in: > my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' ); > > > Any ideas on how to do this under the current API? > > > -Tracy > > _______________________________________________ > 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 Jul 21 22:04:48 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 17:04:48 -0500 Subject: [Bioperl-l] Finding mutations in Blast files In-Reply-To: <29216321.post@talk.nabble.com> References: <29216321.post@talk.nabble.com> Message-ID: <1B5D46EC-BC67-43BB-9376-4A246CB093AD@illinois.edu> On Jul 20, 2010, at 1:36 PM, Gabriel Ab wrote: > > I'm trying to write a script to find mutations in a Blast output file. > The result should look something like [A/G] (query/subject) for SNPs and > [--/AT] for In/Dels. I also need 50 bases both upstream and downstream if > possible. In order to get upstream and downstream you will need access to the original sequence (this information is not reported in the BLAST file). Use the HSP coords to pull that information. > I was able to get both the query and subject sequence extracted from blast > files, but parsing through that for mutations without the help of modules > and writing them like above is harder than it sounds. Deletions and other > things in the alignment can make it very tricky. I tried looking for > modules that would make this task easier but I couldn't find anything. ... > Can someone point me in the right direction on how to do this or let me know > about modules that could help? > > Thanks Bio::Search::HSP::GenericHSP::seq_inds() does something along these lines, e.g. iterates through the two strings by index position and stores relevant information. In this case, you would just print out [X/Y] where there is no match, or [--/XY] when gaps are present. Look at the code for that method to get the general idea. chris From David.Messina at sbc.su.se Wed Jul 21 22:43:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 21 Jul 2010 16:43:07 -0600 Subject: [Bioperl-l] Parsing Alternative Splicing Gene information from Genbank file using Bioperl In-Reply-To: <29203643.post@talk.nabble.com> References: <29203643.post@talk.nabble.com> Message-ID: Hi Amrita, You will want to read the Feature Annotation HOWTO for details of how to parse a Genbank file: http://www.bioperl.org/wiki/HOWTO:Feature-Annotation Dave From cjfields at illinois.edu Thu Jul 22 00:09:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 19:09:05 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: Message-ID: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> It's very possible this is due to API changes within io_lib, but I can't be sure. Aaron, any idea? Just to note, we no longer recommend using the bioperl-ext modules, mainly b/c they have not been actively maintained, so much so that updating them to use the current API is quite difficult (might involve some extensive refactoring). The BioLib project, however, has perl bindings to io_lib. If one had time they could incorporate the BioLib io_lib bindings into bioperl, but I believe ABI support was removed a while ago so that will be problematic. chris On Jul 19, 2010, at 2:11 AM, ??? wrote: > Hi, > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > bioperl-ext-1.5.1, and io-lib-1.8.11; > my OS was 32-bit, Centos 5.2. > When I convert abi-format files to phd-format files, > the value of quality of all bases are '0', and the value of > trace_index of all bases are undefined. > Is there any possible reason leading to this problem? > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > 0.980904.e in phd files; > if this is the case, where can I find phred executers? > > The following is the code utilizing BioPerl and results from BioPerl > and Phred respectively: > ============================================== > #!/usr/bin/perl -w > unshift(@INC, "/opt/BioPerl-1.6.1/"); > unshift(@INC, "/opt/bioperl-ext"); > use strict; > use Bio::SeqIO; > > my $inputfilename='./HMA040184H12.T3.ab1'; > my $outputfilename='test11.phd'; > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > -format => 'abi'); > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > -format => 'phd'); > > while ( my $seq = $in->next_seq() ) { > for my $curr(1 .. $seq->length()) { > print "[",$seq->qualat($curr),"]:"; > print "[",$seq->trace_index_at($curr),"]\t"; > } > $out->write_seq($seq); > last; > } > > ================== test11.phd (by Bio::SeqIO) ================= > BEGIN_SEQUENCE (null) > > BEGIN_COMMENT > > CHROMAT_FILE: unknown > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.980904.e > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Mon Jul 19 11:59:09 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: unknown > CHEM: unknown > DYE: unknown > > END_COMMENT > > BEGIN_DNA > A 0 > G 0 > G 0 > G 0 > G 0 > . > . > . > . > > G 0 > T 0 > T 0 > G 0 > T 0 > C 0 > G 0 > C 0 > T 0 > A 0 > C 0 > END_DNA > > END_SEQUENCE > > ================== .phd (by phred 0.020425.c) ======================= > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > BEGIN_COMMENT > > CHROMAT_FILE: HMA040184H12.T3.ab1 > ABI_THUMBPRINT: 0 > PHRED_VERSION: 0.020425.c > CALL_METHOD: phred > QUALITY_LEVELS: 99 > TIME: Fri Jul 9 16:20:59 2010 > TRACE_ARRAY_MIN_INDEX: 0 > TRACE_ARRAY_MAX_INDEX: 11905 > TRIM: 38 900 0.0500 > TRACE_PEAK_AREA_RATIO: 0.0630 > CHEM: term > DYE: big > > END_COMMENT > > BEGIN_DNA > a 11 2 > g 11 13 > g 11 22 > a 11 37 > a 11 52 > g 8 65 > c 6 76 > t 6 91 > c 6 97 > . > . > . > a 14 11840 > c 16 11849 > a 16 11861 > a 12 11873 > c 12 11885 > g 12 11897 > END_DNA > > END_SEQUENCE > ================================================ > Sincerely yours, > Yen-Chang Chen > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From amackey at virginia.edu Thu Jul 22 00:36:02 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Wed, 21 Jul 2010 20:36:02 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the bioperl-ext modules are not installed? Regardless, can you get a dump of the $seq objects before you hand them off to Bio::SeqIO::phd -- have the qual scores already been lost (problem with the abi reader), or not (problem with the phd writer)? And a basic question -- I assume your .abi files actually have quality values in them (not all do)? -Aaron On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > It's very possible this is due to API changes within io_lib, but I can't be > sure. Aaron, any idea? > > Just to note, we no longer recommend using the bioperl-ext modules, mainly > b/c they have not been actively maintained, so much so that updating them to > use the current API is quite difficult (might involve some extensive > refactoring). The BioLib project, however, has perl bindings to io_lib. If > one had time they could incorporate the BioLib io_lib bindings into bioperl, > but I believe ABI support was removed a while ago so that will be > problematic. > > chris > > On Jul 19, 2010, at 2:11 AM, ??? wrote: > > > Hi, > > > > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > > bioperl-ext-1.5.1, and io-lib-1.8.11; > > my OS was 32-bit, Centos 5.2. > > When I convert abi-format files to phd-format files, > > the value of quality of all bases are '0', and the value of > > trace_index of all bases are undefined. > > Is there any possible reason leading to this problem? > > > > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > > 0.980904.e in phd files; > > if this is the case, where can I find phred executers? > > > > The following is the code utilizing BioPerl and results from BioPerl > > and Phred respectively: > > ============================================== > > #!/usr/bin/perl -w > > unshift(@INC, "/opt/BioPerl-1.6.1/"); > > unshift(@INC, "/opt/bioperl-ext"); > > use strict; > > use Bio::SeqIO; > > > > my $inputfilename='./HMA040184H12.T3.ab1'; > > my $outputfilename='test11.phd'; > > > > my $in = Bio::SeqIO->new(-file => "$inputfilename", > > -format => 'abi'); > > > > my $out = Bio::SeqIO->new(-file => ">$outputfilename", > > -format => 'phd'); > > > > while ( my $seq = $in->next_seq() ) { > > for my $curr(1 .. $seq->length()) { > > print "[",$seq->qualat($curr),"]:"; > > print "[",$seq->trace_index_at($curr),"]\t"; > > } > > $out->write_seq($seq); > > last; > > } > > > > ================== test11.phd (by Bio::SeqIO) ================= > > BEGIN_SEQUENCE (null) > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: unknown > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.980904.e > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Mon Jul 19 11:59:09 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: unknown > > CHEM: unknown > > DYE: unknown > > > > END_COMMENT > > > > BEGIN_DNA > > A 0 > > G 0 > > G 0 > > G 0 > > G 0 > > . > > . > > . > > . > > > > G 0 > > T 0 > > T 0 > > G 0 > > T 0 > > C 0 > > G 0 > > C 0 > > T 0 > > A 0 > > C 0 > > END_DNA > > > > END_SEQUENCE > > > > ================== .phd (by phred 0.020425.c) ======================= > > BEGIN_SEQUENCE HMA040184H12.T3.ab1 > > > > BEGIN_COMMENT > > > > CHROMAT_FILE: HMA040184H12.T3.ab1 > > ABI_THUMBPRINT: 0 > > PHRED_VERSION: 0.020425.c > > CALL_METHOD: phred > > QUALITY_LEVELS: 99 > > TIME: Fri Jul 9 16:20:59 2010 > > TRACE_ARRAY_MIN_INDEX: 0 > > TRACE_ARRAY_MAX_INDEX: 11905 > > TRIM: 38 900 0.0500 > > TRACE_PEAK_AREA_RATIO: 0.0630 > > CHEM: term > > DYE: big > > > > END_COMMENT > > > > BEGIN_DNA > > a 11 2 > > g 11 13 > > g 11 22 > > a 11 37 > > a 11 52 > > g 8 65 > > c 6 76 > > t 6 91 > > c 6 97 > > . > > . > > . > > a 14 11840 > > c 16 11849 > > a 16 11861 > > a 12 11873 > > c 12 11885 > > g 12 11897 > > END_DNA > > > > END_SEQUENCE > > ================================================ > > Sincerely yours, > > Yen-Chang Chen > > > > _______________________________________________ > > 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 Jul 22 02:41:16 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jul 2010 21:41:16 -0500 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> Message-ID: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Nope; doesn't appear to be a pure-perl parser for this. Was there one? chris On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > bioperl-ext modules are not installed? > > Regardless, can you get a dump of the $seq objects before you hand them off > to Bio::SeqIO::phd -- have the qual scores already been lost (problem with > the abi reader), or not (problem with the phd writer)? > > And a basic question -- I assume your .abi files actually have quality > values in them (not all do)? > > -Aaron > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields wrote: > >> It's very possible this is due to API changes within io_lib, but I can't be >> sure. Aaron, any idea? >> >> Just to note, we no longer recommend using the bioperl-ext modules, mainly >> b/c they have not been actively maintained, so much so that updating them to >> use the current API is quite difficult (might involve some extensive >> refactoring). The BioLib project, however, has perl bindings to io_lib. If >> one had time they could incorporate the BioLib io_lib bindings into bioperl, >> but I believe ABI support was removed a while ago so that will be >> problematic. >> >> chris >> >> On Jul 19, 2010, at 2:11 AM, ??? wrote: >> >>> Hi, >>> >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, >>> bioperl-ext-1.5.1, and io-lib-1.8.11; >>> my OS was 32-bit, Centos 5.2. >>> When I convert abi-format files to phd-format files, >>> the value of quality of all bases are '0', and the value of >>> trace_index of all bases are undefined. >>> Is there any possible reason leading to this problem? >>> >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is >>> 0.980904.e in phd files; >>> if this is the case, where can I find phred executers? >>> >>> The following is the code utilizing BioPerl and results from BioPerl >>> and Phred respectively: >>> ============================================== >>> #!/usr/bin/perl -w >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); >>> unshift(@INC, "/opt/bioperl-ext"); >>> use strict; >>> use Bio::SeqIO; >>> >>> my $inputfilename='./HMA040184H12.T3.ab1'; >>> my $outputfilename='test11.phd'; >>> >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", >>> -format => 'abi'); >>> >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", >>> -format => 'phd'); >>> >>> while ( my $seq = $in->next_seq() ) { >>> for my $curr(1 .. $seq->length()) { >>> print "[",$seq->qualat($curr),"]:"; >>> print "[",$seq->trace_index_at($curr),"]\t"; >>> } >>> $out->write_seq($seq); >>> last; >>> } >>> >>> ================== test11.phd (by Bio::SeqIO) ================= >>> BEGIN_SEQUENCE (null) >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: unknown >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.980904.e >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Mon Jul 19 11:59:09 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: unknown >>> CHEM: unknown >>> DYE: unknown >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> A 0 >>> G 0 >>> G 0 >>> G 0 >>> G 0 >>> . >>> . >>> . >>> . >>> >>> G 0 >>> T 0 >>> T 0 >>> G 0 >>> T 0 >>> C 0 >>> G 0 >>> C 0 >>> T 0 >>> A 0 >>> C 0 >>> END_DNA >>> >>> END_SEQUENCE >>> >>> ================== .phd (by phred 0.020425.c) ======================= >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 >>> >>> BEGIN_COMMENT >>> >>> CHROMAT_FILE: HMA040184H12.T3.ab1 >>> ABI_THUMBPRINT: 0 >>> PHRED_VERSION: 0.020425.c >>> CALL_METHOD: phred >>> QUALITY_LEVELS: 99 >>> TIME: Fri Jul 9 16:20:59 2010 >>> TRACE_ARRAY_MIN_INDEX: 0 >>> TRACE_ARRAY_MAX_INDEX: 11905 >>> TRIM: 38 900 0.0500 >>> TRACE_PEAK_AREA_RATIO: 0.0630 >>> CHEM: term >>> DYE: big >>> >>> END_COMMENT >>> >>> BEGIN_DNA >>> a 11 2 >>> g 11 13 >>> g 11 22 >>> a 11 37 >>> a 11 52 >>> g 8 65 >>> c 6 76 >>> t 6 91 >>> c 6 97 >>> . >>> . >>> . >>> a 14 11840 >>> c 16 11849 >>> a 16 11861 >>> a 12 11873 >>> c 12 11885 >>> g 12 11897 >>> END_DNA >>> >>> END_SEQUENCE >>> ================================================ >>> Sincerely yours, >>> Yen-Chang Chen >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 alperyilmaz at gmail.com Thu Jul 22 04:09:38 2010 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Thu, 22 Jul 2010 00:09:38 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO Message-ID: Hi, I was using Bio::SeqIO with perl one-liner and I noticed an oddity. Can someone suggest a correction or workaround? Let test.fa be; >1 AGTC >2 CTGA Then, commandline below prints the expected output: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < test.fa output: 1 AGTC 2 CTGA However, if use the command in a pipe, then the output has an issue with primary_id of initial sequence. $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' output: AGTC 2 CTGA What is the workaround to make Bio::SeqIO work correctly in a one-liner with pipes? thanks, Alper Yilmaz Post-doctoral Researcher Plant Biotechnology Center The Ohio State University 1060 Carmack Rd Columbus, OH 43210 (614)688-4954 PS: Normally, the example is demonstrating useless use of cat, for the sake giving an example, it can be "command1 | command2 | command3 | perl -MBioSeqIO -e'...' " instead.. From fs5 at sanger.ac.uk Thu Jul 22 10:48:25 2010 From: fs5 at sanger.ac.uk (Frank Schwach) Date: Thu, 22 Jul 2010 11:48:25 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: Message-ID: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Hi Alper, You can actually reproduce it also by providing STDIN from keyboard input like so: $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >1 aaaaaaaaa >2 aaaaaaaaa ggggggggg >3 2 ggggggggg ccccccccc 3 ccccccccc In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} then the command returned the sequence of the first entry without the ID again. >From the second entry onwards, it is all correct. I'm not 100% sure but could it be linked to buffering? SeqIO has to read ahead to find a complete entry that spans multiple lines. When you get STDIN from a file, you will get buffering and receive more than one line at once, which will allow the next_seq method to work as expected. If you provide line-by-line input then that method probably can't work correctly. If that is the case then you can't use the command in a pipe at all. Frank On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: > Hi, > > I was using Bio::SeqIO with perl one-liner and I noticed an oddity. > Can someone suggest a correction or workaround? > > Let test.fa be; > >1 > AGTC > >2 > CTGA > > Then, commandline below prints the expected output: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' < > test.fa > > output: > 1 AGTC > 2 CTGA > > However, if use the command in a pipe, then the output has an issue > with primary_id of initial sequence. > $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > =>\*STDIN); while ($myseq=$seq->next_seq){ print > $myseq->id,"\t",$myseq->seq,"\n"}' > > output: > AGTC > 2 CTGA > > What is the workaround to make Bio::SeqIO work correctly in a > one-liner with pipes? > > thanks, > > Alper Yilmaz > Post-doctoral Researcher > Plant Biotechnology Center > The Ohio State University > 1060 Carmack Rd > Columbus, OH 43210 > (614)688-4954 > > > PS: Normally, the example is demonstrating useless use of cat, for the > sake giving an example, it can be "command1 | command2 | command3 | > perl -MBioSeqIO -e'...' " instead.. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- 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 roy.chaudhuri at gmail.com Thu Jul 22 11:49:41 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 12:49:41 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> Message-ID: <4C483055.5050402@gmail.com> Hi Alper, The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. Cheers. Roy. On 22/07/2010 11:48, Frank Schwach wrote: > Hi Alper, > > You can actually reproduce it also by providing STDIN from keyboard > input like so: > $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while > ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >> 1 > aaaaaaaaa >> 2 > aaaaaaaaa > ggggggggg >> 3 > 2 ggggggggg > ccccccccc > 3 ccccccccc > > In this case I typed > ">1"[ENTER] > "aaaaaaaaa"[ENTER] > ">2"[ENTER} > then the command returned the sequence of the first entry without the ID > again. >> From the second entry onwards, it is all correct. > > I'm not 100% sure but could it be linked to buffering? SeqIO has to read > ahead to find a complete entry that spans multiple lines. When you get > STDIN from a file, you will get buffering and receive more than one line > at once, which will allow the next_seq method to work as expected. If > you provide line-by-line input then that method probably can't work > correctly. > If that is the case then you can't use the command in a pipe at all. > > Frank > > > > On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >> Hi, >> >> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >> Can someone suggest a correction or workaround? >> >> Let test.fa be; >>> 1 >> AGTC >>> 2 >> CTGA >> >> Then, commandline below prints the expected output: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >> test.fa >> >> output: >> 1 AGTC >> 2 CTGA >> >> However, if use the command in a pipe, then the output has an issue >> with primary_id of initial sequence. >> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> $myseq->id,"\t",$myseq->seq,"\n"}' >> >> output: >> AGTC >> 2 CTGA >> >> What is the workaround to make Bio::SeqIO work correctly in a >> one-liner with pipes? >> >> thanks, >> >> Alper Yilmaz >> Post-doctoral Researcher >> Plant Biotechnology Center >> The Ohio State University >> 1060 Carmack Rd >> Columbus, OH 43210 >> (614)688-4954 >> >> >> PS: Normally, the example is demonstrating useless use of cat, for the >> sake giving an example, it can be "command1 | command2 | command3 | >> perl -MBioSeqIO -e'...' " instead.. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From amackey at virginia.edu Thu Jul 22 13:19:52 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 09:19:52 -0400 Subject: [Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO In-Reply-To: <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> References: <4A10916F-4A87-4545-A27F-FE921AFF05F4@illinois.edu> <178E659D-B53B-4176-992D-9FF75DEDB14C@illinois.edu> Message-ID: Hmm, perhaps I'm thinking about the SCF code, not the ABI code. -Aaron On Wed, Jul 21, 2010 at 10:41 PM, Chris Fields wrote: > Nope; doesn't appear to be a pure-perl parser for this. Was there one? > > chris > > On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote: > > > Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the > > bioperl-ext modules are not installed? > > > > Regardless, can you get a dump of the $seq objects before you hand them > off > > to Bio::SeqIO::phd -- have the qual scores already been lost (problem > with > > the abi reader), or not (problem with the phd writer)? > > > > And a basic question -- I assume your .abi files actually have quality > > values in them (not all do)? > > > > -Aaron > > > > > > On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields > wrote: > > > >> It's very possible this is due to API changes within io_lib, but I can't > be > >> sure. Aaron, any idea? > >> > >> Just to note, we no longer recommend using the bioperl-ext modules, > mainly > >> b/c they have not been actively maintained, so much so that updating > them to > >> use the current API is quite difficult (might involve some extensive > >> refactoring). The BioLib project, however, has perl bindings to io_lib. > If > >> one had time they could incorporate the BioLib io_lib bindings into > bioperl, > >> but I believe ABI support was removed a while ago so that will be > >> problematic. > >> > >> chris > >> > >> On Jul 19, 2010, at 2:11 AM, ??? wrote: > >> > >>> Hi, > >>> > >>> I'm processing chromate files (.ab1 format) with BioPerl-1.6.1, > >>> bioperl-ext-1.5.1, and io-lib-1.8.11; > >>> my OS was 32-bit, Centos 5.2. > >>> When I convert abi-format files to phd-format files, > >>> the value of quality of all bases are '0', and the value of > >>> trace_index of all bases are undefined. > >>> Is there any possible reason leading to this problem? > >>> > >>> Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is > >>> 0.980904.e in phd files; > >>> if this is the case, where can I find phred executers? > >>> > >>> The following is the code utilizing BioPerl and results from BioPerl > >>> and Phred respectively: > >>> ============================================== > >>> #!/usr/bin/perl -w > >>> unshift(@INC, "/opt/BioPerl-1.6.1/"); > >>> unshift(@INC, "/opt/bioperl-ext"); > >>> use strict; > >>> use Bio::SeqIO; > >>> > >>> my $inputfilename='./HMA040184H12.T3.ab1'; > >>> my $outputfilename='test11.phd'; > >>> > >>> my $in = Bio::SeqIO->new(-file => "$inputfilename", > >>> -format => 'abi'); > >>> > >>> my $out = Bio::SeqIO->new(-file => ">$outputfilename", > >>> -format => 'phd'); > >>> > >>> while ( my $seq = $in->next_seq() ) { > >>> for my $curr(1 .. $seq->length()) { > >>> print "[",$seq->qualat($curr),"]:"; > >>> print "[",$seq->trace_index_at($curr),"]\t"; > >>> } > >>> $out->write_seq($seq); > >>> last; > >>> } > >>> > >>> ================== test11.phd (by Bio::SeqIO) ================= > >>> BEGIN_SEQUENCE (null) > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: unknown > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.980904.e > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Mon Jul 19 11:59:09 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: unknown > >>> CHEM: unknown > >>> DYE: unknown > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> A 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> G 0 > >>> . > >>> . > >>> . > >>> . > >>> > >>> G 0 > >>> T 0 > >>> T 0 > >>> G 0 > >>> T 0 > >>> C 0 > >>> G 0 > >>> C 0 > >>> T 0 > >>> A 0 > >>> C 0 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> > >>> ================== .phd (by phred 0.020425.c) ======================= > >>> BEGIN_SEQUENCE HMA040184H12.T3.ab1 > >>> > >>> BEGIN_COMMENT > >>> > >>> CHROMAT_FILE: HMA040184H12.T3.ab1 > >>> ABI_THUMBPRINT: 0 > >>> PHRED_VERSION: 0.020425.c > >>> CALL_METHOD: phred > >>> QUALITY_LEVELS: 99 > >>> TIME: Fri Jul 9 16:20:59 2010 > >>> TRACE_ARRAY_MIN_INDEX: 0 > >>> TRACE_ARRAY_MAX_INDEX: 11905 > >>> TRIM: 38 900 0.0500 > >>> TRACE_PEAK_AREA_RATIO: 0.0630 > >>> CHEM: term > >>> DYE: big > >>> > >>> END_COMMENT > >>> > >>> BEGIN_DNA > >>> a 11 2 > >>> g 11 13 > >>> g 11 22 > >>> a 11 37 > >>> a 11 52 > >>> g 8 65 > >>> c 6 76 > >>> t 6 91 > >>> c 6 97 > >>> . > >>> . > >>> . > >>> a 14 11840 > >>> c 16 11849 > >>> a 16 11861 > >>> a 12 11873 > >>> c 12 11885 > >>> g 12 11897 > >>> END_DNA > >>> > >>> END_SEQUENCE > >>> ================================================ > >>> Sincerely yours, > >>> Yen-Chang Chen > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/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 Jul 22 13:27:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 08:27:30 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C483055.5050402@gmail.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> Message-ID: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Would someone like to file this as a bug? My guess is this may be a combination of using pipes and the way FASTA is parsed (locally resets $/). http://bugzilla.open-bio.org chris On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > Hi Alper, > > The problem comes about because you don't specify -format=>'fasta' in your Bio::SeqIO object. BioPerl attempts to guess the format if you don't specify it, but seems to be struggling in this case. I can't really think of any good reason for not specifying the format. Just in case anyone wants to investigate further, I noticed that if you try the example with longer fasta sequences, the first line of the sequence is interpreted as the id, with the remainder as the sequence. > > Cheers. > Roy. > > On 22/07/2010 11:48, Frank Schwach wrote: >> Hi Alper, >> >> You can actually reproduce it also by providing STDIN from keyboard >> input like so: >> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}' >>> 1 >> aaaaaaaaa >>> 2 >> aaaaaaaaa >> ggggggggg >>> 3 >> 2 ggggggggg >> ccccccccc >> 3 ccccccccc >> >> In this case I typed >> ">1"[ENTER] >> "aaaaaaaaa"[ENTER] >> ">2"[ENTER} >> then the command returned the sequence of the first entry without the ID >> again. >>> From the second entry onwards, it is all correct. >> >> I'm not 100% sure but could it be linked to buffering? SeqIO has to read >> ahead to find a complete entry that spans multiple lines. When you get >> STDIN from a file, you will get buffering and receive more than one line >> at once, which will allow the next_seq method to work as expected. If >> you provide line-by-line input then that method probably can't work >> correctly. >> If that is the case then you can't use the command in a pipe at all. >> >> Frank >> >> >> >> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>> Hi, >>> >>> I was using Bio::SeqIO with perl one-liner and I noticed an oddity. >>> Can someone suggest a correction or workaround? >>> >>> Let test.fa be; >>>> 1 >>> AGTC >>>> 2 >>> CTGA >>> >>> Then, commandline below prints the expected output: >>> $ perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print $myseq->id,"\t",$myseq->seq,"\n"}'< >>> test.fa >>> >>> output: >>> 1 AGTC >>> 2 CTGA >>> >>> However, if use the command in a pipe, then the output has an issue >>> with primary_id of initial sequence. >>> $ cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>> >>> output: >>> AGTC >>> 2 CTGA >>> >>> What is the workaround to make Bio::SeqIO work correctly in a >>> one-liner with pipes? >>> >>> thanks, >>> >>> Alper Yilmaz >>> Post-doctoral Researcher >>> Plant Biotechnology Center >>> The Ohio State University >>> 1060 Carmack Rd >>> Columbus, OH 43210 >>> (614)688-4954 >>> >>> >>> PS: Normally, the example is demonstrating useless use of cat, for the >>> sake giving an example, it can be "command1 | command2 | command3 | >>> perl -MBioSeqIO -e'...' " instead.. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/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 roy.chaudhuri at gmail.com Thu Jul 22 13:41:00 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 22 Jul 2010 14:41:00 +0100 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C484A6C.1000502@gmail.com> Done (bug 3122). On 22/07/2010 14:27, Chris Fields wrote: > Would someone like to file this as a bug? My guess is this may be a > combination of using pipes and the way FASTA is parsed (locally > resets $/). > > http://bugzilla.open-bio.org > > chris > > On Jul 22, 2010, at 6:49 AM, Roy Chaudhuri wrote: > >> Hi Alper, >> >> The problem comes about because you don't specify -format=>'fasta' >> in your Bio::SeqIO object. BioPerl attempts to guess the format if >> you don't specify it, but seems to be struggling in this case. I >> can't really think of any good reason for not specifying the >> format. Just in case anyone wants to investigate further, I noticed >> that if you try the example with longer fasta sequences, the first >> line of the sequence is interpreted as the id, with the remainder >> as the sequence. >> >> Cheers. Roy. >> >> On 22/07/2010 11:48, Frank Schwach wrote: >>> Hi Alper, >>> >>> You can actually reproduce it also by providing STDIN from >>> keyboard input like so: $ perl -MBio::SeqIO -e 'my >>> $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>> ($myseq=$seq->next_seq){ print >>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> 1 >>> aaaaaaaaa >>>> 2 >>> aaaaaaaaa ggggggggg >>>> 3 >>> 2 ggggggggg ccccccccc 3 ccccccccc >>> >>> In this case I typed ">1"[ENTER] "aaaaaaaaa"[ENTER] ">2"[ENTER} >>> then the command returned the sequence of the first entry without >>> the ID again. >>>> From the second entry onwards, it is all correct. >>> >>> I'm not 100% sure but could it be linked to buffering? SeqIO has >>> to read ahead to find a complete entry that spans multiple lines. >>> When you get STDIN from a file, you will get buffering and >>> receive more than one line at once, which will allow the next_seq >>> method to work as expected. If you provide line-by-line input >>> then that method probably can't work correctly. If that is the >>> case then you can't use the command in a pipe at all. >>> >>> Frank >>> >>> >>> >>> On Thu, 2010-07-22 at 00:09 -0400, Alper Yilmaz wrote: >>>> Hi, >>>> >>>> I was using Bio::SeqIO with perl one-liner and I noticed an >>>> oddity. Can someone suggest a correction or workaround? >>>> >>>> Let test.fa be; >>>>> 1 >>>> AGTC >>>>> 2 >>>> CTGA >>>> >>>> Then, commandline below prints the expected output: $ perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}'< test.fa >>>> >>>> output: 1 AGTC 2 CTGA >>>> >>>> However, if use the command in a pipe, then the output has an >>>> issue with primary_id of initial sequence. $ cat test.fa | perl >>>> -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh =>\*STDIN); while >>>> ($myseq=$seq->next_seq){ print >>>> $myseq->id,"\t",$myseq->seq,"\n"}' >>>> >>>> output: AGTC 2 CTGA >>>> >>>> What is the workaround to make Bio::SeqIO work correctly in a >>>> one-liner with pipes? >>>> >>>> thanks, >>>> >>>> Alper Yilmaz Post-doctoral Researcher Plant Biotechnology >>>> Center The Ohio State University 1060 Carmack Rd Columbus, OH >>>> 43210 (614)688-4954 >>>> >>>> >>>> PS: Normally, the example is demonstrating useless use of cat, >>>> for the sake giving an example, it can be "command1 | command2 >>>> | command3 | perl -MBioSeqIO -e'...' " instead.. >>>> _______________________________________________ Bioperl-l >>>> mailing list Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/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 sheetu.piscean at gmail.com Wed Jul 21 21:49:25 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Wed, 21 Jul 2010 14:49:25 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Adding some more details on OS and BioPerl version OS: sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 UTC 2010 i686 GNU/Linux Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi BioPerl Version : sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' 1.006001 Attached is the error that I get while running the RemoteBlast. Thanks, Sheetal On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani wrote: > Hi, > > I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > is the complete script : > #Remote-blast "factory object" creation and blast-parameter > initialization > > use Bio::Tools::Run::RemoteBlast; > use strict; > my $prog = 'blastx'; > my $db = 'nr/nt'; > my $e_val= '1e-10'; > > my @params = ( '-prog' => $prog, > '-data' => $db, > '-expect' => $e_val, > '-readmethod' => 'SearchIO' ); > > my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > #$v is just to turn on and off the messages > my $v = 0; > > my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > ); > > while (my $input = $str->next_seq()){ > #Blast a sequence against a database: > > #Alternatively, you could pass in a file with many > #sequences rather than loop through sequence one at a time > #Remove the loop starting 'while (my $input = $str->next_seq())' > #and swap the two lines below for an example of that. > my $r = $factory->submit_blast($input); > #my $r = $factory->submit_blast('amino.fa'); > > print STDERR "waiting..." if( $v > 0 ); > while ( my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = $factory->retrieve_blast($rid); > if( !ref($rc) ) { > if( $rc < 0 ) { > print "removing rid as rc is < 0"; > $factory->remove_rid($rid); > } > print STDERR "." if ( $v > 0 ); > sleep 5; > } else { > my $result = $rc->next_result(); > #save the output > print "saving to file"; > my $filename = "contig_236.out"; #$result->query_name()."\.out"; > $factory->save_output($filename); > $factory->remove_rid($rid); > print "\nQuery Name: ", $result->query_name(), "\n"; > while ( my $hit = $result->next_hit ) { > next unless ( $v > 0); > print "\thit name is ", $hit->name, "\n"; > while( my $hsp = $hit->next_hsp ) { > print "\t\tscore is ", $hsp->score, "\n"; > } > } > } > } > } > } > > But when I run this, I get an error in html format which says "Cannot > accept request, error code: -103". Attaching the error file for reference. > Can you please help me with debugging this error? Your help is much > appreciated. > > Also, informing about the previous error that I fixed by adding this line: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > I was getting prior to adding this line was : > --------------------- WARNING --------------------- > MSG:

An error has occurred on the > server, The server is unable to format right now, please try again in a few > minutes. If the problem (Informational Message: No alias or index file > found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4CF5MY9101P

> > It kinda took me a while to find out the 2 requirements > > # 1) set your database like this: > -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > > # 2) add this line before submitting the job: > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > I think it will be great if you can add this to the synopsis section of > RemoteBlast.pm > > Thanks, > Sheetal > -------------- next part -------------- An HTML attachment was scrubbed... URL: From evelyne.c88 at gmail.com Thu Jul 22 13:57:47 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 06:57:47 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> Message-ID: <29237193.post@talk.nabble.com> Hi, I would like to run a SW alignment, but i'm new to programming... Tried using several tutorials to install this Bioperl-ext package, but not getting that far... Maybe you can help? -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29237193.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From biopython at maubp.freeserve.co.uk Thu Jul 22 14:41:21 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 15:41:21 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29237193.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: > > Hi, > > I would like to run a SW alignment, but i'm new to programming... > Tried using several tutorials to install this Bioperl-ext package, but not > getting that far... > Maybe you can help? How about using the water tool in EMBOSS? I'm sure BioPerl has wrappers for that... http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html Peter From cjfields at illinois.edu Thu Jul 22 15:31:30 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 10:31:30 -0500 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: On Jul 22, 2010, at 9:41 AM, Peter wrote: > On Thu, Jul 22, 2010 at 2:57 PM, Evelyne wrote: >> >> Hi, >> >> I would like to run a SW alignment, but i'm new to programming... >> Tried using several tutorials to install this Bioperl-ext package, but not >> getting that far... >> Maybe you can help? > > How about using the water tool in EMBOSS? I'm sure BioPerl has > wrappers for that... > > http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/water.html > > Peter Yes, we do. I would suggest that solution as well; the SW work in bioperl-ext hasn't been maintained actively for a while. That doesn't mean it won't suit your needs, but issues with compilation will likely remained unaddressed. chris From evelyne.c88 at gmail.com Thu Jul 22 14:09:30 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 07:09:30 -0700 (PDT) Subject: [Bioperl-l] installing Bioperl-ext package (Bio::Tools::pSW) Message-ID: <29237314.post@talk.nabble.com> Hi I'm kind of a rookie at programming, but i'm trying to align two sequences. And i would like to use Bio::Tools::pSW I have followed instructions and installed a C compiler (devC++) I read a lot of different tutorials, but cannot find a way to install this package, everything i try gives errors latest error when i tried 'install B/BIRNEY/bioperl-ext-1.4.tar.gz' : c:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site' returned status 512, won't make running make test make had some problems, won't test running make install make had some problems, won't install -- View this message in context: http://old.nabble.com/installing-Bioperl-ext-package-%28Bio%3A%3ATools%3A%3ApSW%29-tp29237314p29237314.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From evelyne.c88 at gmail.com Thu Jul 22 15:21:17 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:21:17 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> Message-ID: <29238161.post@talk.nabble.com> I have really no idea what that means... Studying first year of bio-informatics, and have to make a small perl program as exam Maybe I'm in a bit over my head, I'll ask the tutor for some advice... < References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> Message-ID: <4C4855EE.1010208@bms.com> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm if (defined $self->{-file}) { # Close the file we opened. close($fh); } elsif (ref $fh eq 'GLOB') { # Try seeking to the start position. >>> seek($fh, $start_pos, 0); } elsif (defined $fh && $fh->can('setpos')) { # Seek to the start position. $fh->setpos($start_pos); } return ($done ? $fmt_string : undef); seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset is where the second non-null line starts. I am not sure why- all manuals claim this should work? Hope this helps. Stefan On 7/22/2010 9:27 AM, Chris Fields wrote: > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From biopython at maubp.freeserve.co.uk Thu Jul 22 15:42:25 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 22 Jul 2010 16:42:25 +0100 Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: <29238161.post@talk.nabble.com> References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: > > I have really no idea what that means... > Studying first year of bio-informatics, and have to make a small perl > program as exam > Maybe I'm in a bit over my head, I'll ask the tutor for some advice... > The EMBOSS project is a collection of open source command line tools written in C, and includes a tool called "water" for doing Smith Waterman (SW) sequence alignments. I was suggesting you could use BioPerl to call this needle program and parse its output. However, it sounds like you actually have a programming assignment where the point is to actually implement the SW algorithm yourself (in perl). In this case, EMBOSS won't be useful after all. Peter From evelyne.c88 at gmail.com Thu Jul 22 15:53:39 2010 From: evelyne.c88 at gmail.com (Evelyne) Date: Thu, 22 Jul 2010 08:53:39 -0700 (PDT) Subject: [Bioperl-l] Running Smith Waterman alignments in BioPerl In-Reply-To: References: <97B95E8A-9E93-471F-B7FB-31D5D226D104@sgul.ac.uk> <29237193.post@talk.nabble.com> <29238161.post@talk.nabble.com> Message-ID: <29238557.post@talk.nabble.com> There is actually no real assignment with a goal described. We only have to prove that we understand and can use Perl. (Description of the course states we are to learn the concepts of computer programming, and rudimentary Perl) The Smith Waterman Tool was mentioned during the courses (along with BPlite, and using remote and local BLASTs) so i wanted to explore this, without really knowing how complicated the use of this could be... Maybe they just wanted to let us know what possibilities there are, without expecting that we could do this on our own... Peter-329 wrote: > > On Thu, Jul 22, 2010 at 4:21 PM, Evelyne wrote: >> >> I have really no idea what that means... >> Studying first year of bio-informatics, and have to make a small perl >> program as exam >> Maybe I'm in a bit over my head, I'll ask the tutor for some advice... >> > > The EMBOSS project is a collection of open source command line > tools written in C, and includes a tool called "water" for doing Smith > Waterman (SW) sequence alignments. I was suggesting you could > use BioPerl to call this needle program and parse its output. > > However, it sounds like you actually have a programming assignment > where the point is to actually implement the SW algorithm yourself (in > perl). In this case, EMBOSS won't be useful after all. > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- View this message in context: http://old.nabble.com/Running-Smith-Waterman-alignments-in-BioPerl-tp28044312p29238557.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From amackey at virginia.edu Thu Jul 22 17:15:18 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Thu, 22 Jul 2010 13:15:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C4855EE.1010208@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. -Aaron On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov wrote: > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh after reset > is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> > > > _______________________________________________ > 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 Jul 22 18:35:51 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 13:35:51 -0500 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: <4C48853F.3050904@bms.com> References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): tell() on pipes, fifos, and sockets usually returns -1. My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: if (!$self->seekable) { #die a horrible death } chris On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). > I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) > I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. > Another option is to right to a temp file or slurp into memory. This could be dangerous though... > > On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >> >> -Aaron >> >> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: >> >> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >> >> if (defined $self->{-file}) { >> # Close the file we opened. >> close($fh); >> } elsif (ref $fh eq 'GLOB') { >> # Try seeking to the start position. >> >>> seek($fh, $start_pos, 0); >> } elsif (defined $fh && $fh->can('setpos')) { >> # Seek to the start position. >> $fh->setpos($start_pos); >> } >> return ($done ? $fmt_string : undef); >> >> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >> after reset is where the second non-null line starts. >> I am not sure why- all manuals claim this should work? >> Hope this helps. >> Stefan >> >> On 7/22/2010 9:27 AM, Chris Fields wrote: >> >> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >> >>> $myseq->id,"\t",$myseq->seq,"\n"} >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > From dunlopjp.ctr at afrl.hpc.mil Thu Jul 22 16:35:01 2010 From: dunlopjp.ctr at afrl.hpc.mil (Mr. James P. Dunlop (Contractor)) Date: Thu, 22 Jul 2010 12:35:01 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org Message-ID: <4C487335.4080808@afrl.hpc.mil> Hello I very new to this type of install. I am trying to install this as non root, which may be part of the problem, but I thought I found some information that addresses this. Also I'm trying to use cpan. The error before termination is: Files=44, Tests=1140, 30 wallclock secs (22.97 cusr + 6.94 csys = 29.91 CPU) /usr/bin/make test -- OK Running make install /usr/bin/perl Build --makefile_env_macros 1 install Building Module-Build Writing /app/bioperl/BioPerl-1.6.0/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Module/Build/.packlist /usr/bin/make install -- OK Couldn't install Module::Build, giving up. Running make test Make had some problems, maybe interrupted? Won't test Running make install Make had some problems, maybe interrupted? Won't install cpan> Is there anything that is obvious to you folks? Would it be possible to cc any e-mails to dunlopjp at aol.com? Thanks Jim Dunlop 937-255-0050 From stefan.kirov at bms.com Thu Jul 22 17:51:59 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 13:51:59 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> Message-ID: <4C48853F.3050904@bms.com> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. Another option is to right to a temp file or slurp into memory. This could be dangerous though... On 7/22/2010 1:15 PM, Aaron Mackey wrote: > You cannot seek on a pipe, unfortunately. SeqIO should probably try > to detect this, and die rather than invoking GuessSeqFormat. > > -Aaron > > On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov > wrote: > > From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm > > if (defined $self->{-file}) { > # Close the file we opened. > close($fh); > } elsif (ref $fh eq 'GLOB') { > # Try seeking to the start position. > >>> seek($fh, $start_pos, 0); > } elsif (defined $fh && $fh->can('setpos')) { > # Seek to the start position. > $fh->setpos($start_pos); > } > return ($done ? $fmt_string : undef); > > seek($fh, $start_pos, 0); does not reset as expected- tell $fh > after reset is where the second non-null line starts. > I am not sure why- all manuals claim this should work? > Hope this helps. > Stefan > > On 7/22/2010 9:27 AM, Chris Fields wrote: > > cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh > >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print > >>> $myseq->id,"\t",$myseq->seq,"\n"} > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From stefan.kirov at bms.com Thu Jul 22 19:37:18 2010 From: stefan.kirov at bms.com (Stefan Kirov) Date: Thu, 22 Jul 2010 15:37:18 -0400 Subject: [Bioperl-l] perl one-liner with Bio::SeqIO In-Reply-To: References: <1279795705.27211.29.camel@deskpro15336.dynamic.sanger.ac.uk> <4C483055.5050402@gmail.com> <13DA41BD-12EA-456E-BE9F-CEDAEA504757@illinois.edu> <4C4855EE.1010208@bms.com> <4C48853F.3050904@bms.com> Message-ID: <4C489DEE.1010806@bms.com> Chris, I tested tell and for me it actually returns the correct position. I think seek($fh, $start_pos, 0) || $self->throw("Failed resetting the filehandle pointer; IO error occurred"); might be better. On 7/22/2010 2:35 PM, Chris Fields wrote: > It's fairly easy to check if something is seekable, using tell() (from perldoc -f tell): > > tell() on pipes, fifos, and sockets usually returns -1. > > My guess is this is something that should be really be handled by Bio::Root::IO, then SeqIO could check this: > > if (!$self->seekable) { > #die a horrible death > } > > chris > > On Jul 22, 2010, at 12:51 PM, Stefan Kirov wrote: > > >> Sorry for copying you all, but my posts to bioperl list do not go through (my headers seem suspicious). >> I proposed (comment on the bug) that seek throws an IO error, I think this would be good practice in general (device gets disconnected, etc.) >> I agree with Aaron that one option would be that if STDIN is the input format MUST be specified or parser dies. >> Another option is to right to a temp file or slurp into memory. This could be dangerous though... >> >> On 7/22/2010 1:15 PM, Aaron Mackey wrote: >> >>> You cannot seek on a pipe, unfortunately. SeqIO should probably try to detect this, and die rather than invoking GuessSeqFormat. >>> >>> -Aaron >>> >>> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov> wrote: >>> >>> From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm >>> >>> if (defined $self->{-file}) { >>> # Close the file we opened. >>> close($fh); >>> } elsif (ref $fh eq 'GLOB') { >>> # Try seeking to the start position. >>> >>> seek($fh, $start_pos, 0); >>> } elsif (defined $fh&& $fh->can('setpos')) { >>> # Seek to the start position. >>> $fh->setpos($start_pos); >>> } >>> return ($done ? $fmt_string : undef); >>> >>> seek($fh, $start_pos, 0); does not reset as expected- tell $fh >>> after reset is where the second non-null line starts. >>> I am not sure why- all manuals claim this should work? >>> Hope this helps. >>> Stefan >>> >>> On 7/22/2010 9:27 AM, Chris Fields wrote: >>> >>> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh >>> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print >>> >>> $myseq->id,"\t",$myseq->seq,"\n"} >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >> >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: stefan_kirov.vcf Type: text/x-vcard Size: 207 bytes Desc: not available URL: From cjfields at illinois.edu Thu Jul 22 23:54:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 18:54:20 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? chris On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > Adding some more details on OS and BioPerl version > > OS: > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > UTC 2010 i686 GNU/Linux > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > BioPerl Version : > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > 'print $Bio::Root::Version::VERSION,"\n"' > 1.006001 > > Attached is the error that I get while running the RemoteBlast. > > Thanks, > Sheetal > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > wrote: > >> Hi, >> >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here >> is the complete script : >> #Remote-blast "factory object" creation and blast-parameter >> initialization >> >> use Bio::Tools::Run::RemoteBlast; >> use strict; >> my $prog = 'blastx'; >> my $db = 'nr/nt'; >> my $e_val= '1e-10'; >> >> my @params = ( '-prog' => $prog, >> '-data' => $db, >> '-expect' => $e_val, >> '-readmethod' => 'SearchIO' ); >> >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); >> >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; >> >> #$v is just to turn on and off the messages >> my $v = 0; >> >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' >> ); >> >> while (my $input = $str->next_seq()){ >> #Blast a sequence against a database: >> >> #Alternatively, you could pass in a file with many >> #sequences rather than loop through sequence one at a time >> #Remove the loop starting 'while (my $input = $str->next_seq())' >> #and swap the two lines below for an example of that. >> my $r = $factory->submit_blast($input); >> #my $r = $factory->submit_blast('amino.fa'); >> >> print STDERR "waiting..." if( $v > 0 ); >> while ( my @rids = $factory->each_rid ) { >> foreach my $rid ( @rids ) { >> my $rc = $factory->retrieve_blast($rid); >> if( !ref($rc) ) { >> if( $rc < 0 ) { >> print "removing rid as rc is < 0"; >> $factory->remove_rid($rid); >> } >> print STDERR "." if ( $v > 0 ); >> sleep 5; >> } else { >> my $result = $rc->next_result(); >> #save the output >> print "saving to file"; >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; >> $factory->save_output($filename); >> $factory->remove_rid($rid); >> print "\nQuery Name: ", $result->query_name(), "\n"; >> while ( my $hit = $result->next_hit ) { >> next unless ( $v > 0); >> print "\thit name is ", $hit->name, "\n"; >> while( my $hsp = $hit->next_hsp ) { >> print "\t\tscore is ", $hsp->score, "\n"; >> } >> } >> } >> } >> } >> } >> >> But when I run this, I get an error in html format which says "Cannot >> accept request, error code: -103". Attaching the error file for reference. >> Can you please help me with debugging this error? Your help is much >> appreciated. >> >> Also, informing about the previous error that I fixed by adding this line: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that >> I was getting prior to adding this line was : >> --------------------- WARNING --------------------- >> MSG:

An error has occurred on the >> server, The server is unable to format right now, please try again in a few >> minutes. If the problem (Informational Message: No alias or index file >> found for protein database [nr/nt] in search path >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: >> 4CF5MY9101P

>> >> It kinda took me a while to find out the 2 requirements >> >> # 1) set your database like this: >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options >> >> >> # 2) add this line before submitting the job: >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; >> >> I think it will be great if you can add this to the synopsis section of >> RemoteBlast.pm >> >> Thanks, >> Sheetal >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Thu Jul 22 23:52:19 2010 From: genehack at genehack.org (John Anderson) Date: Thu, 22 Jul 2010 19:52:19 -0400 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: <4C487335.4080808@afrl.hpc.mil> References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: The one thing that sticks out is this: > Couldn't install Module::Build, giving up. Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. chrs, john. From cjfields at illinois.edu Fri Jul 23 01:53:36 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:53:36 -0500 Subject: [Bioperl-l] Installing bioperl-l@bioperl.org In-Reply-To: References: <4C487335.4080808@afrl.hpc.mil> Message-ID: On Jul 22, 2010, at 6:52 PM, John Anderson wrote: > > On Jul 22, 2010, at 12:35 PM, Mr. James P. Dunlop (Contractor) wrote: > > The one thing that sticks out is this: > >> Couldn't install Module::Build, giving up. > > Try installing Module::Build by hand, and make sure you've got things set up to install under $HOME rather than some system directory you don't have write permissions for. > > chrs, > john. Also helps to set any CPAN configuration to install locally. http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA chris From cjfields at illinois.edu Fri Jul 23 01:52:15 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jul 2010 20:52:15 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Removing this line from your original script worked for me: $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; This is set via '-prog' parameter. chris On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". > > Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : > An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > Adding below the email conversation with blast-help for debugging further : > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: > Sheetal, > > You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. > > Best regards, > Wayne > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. > > The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. > > Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. > > Thanks, > Sheetal > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: > Hello, > > Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > Best regards, > Wayne > > _~___~___~__~__~_~ > Wayne Matten, PhD > NCBI Public Services > mattenw at mail.nih.gov > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > Hello, > > I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : > Cannot accept request, error code: -103 > > The request that I send is : > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx >> >> Can you please help me debug it. >> >> Thanks and Regards, >> Sheetal > > Thanks > Sheetal > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sheetu.piscean at gmail.com Fri Jul 23 00:30:24 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Thu, 22 Jul 2010 17:30:24 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: Yes the error is still occurring. I have emailed to Blast-help as well and they have to say that "there is something wrong with the URL, didn't give any specifics". Also changing the parameter SERVICE to 'plain' (by default it is set to plain, I guess this value is for standard blast pgm. like blastp, blastx, etc) gives me this error : An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. Adding below the email conversation with blast-help for debugging further : On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten wrote: Sheetal, You are right about the query syntax, but your URL has some errors. The URL below works; note that order of parameters does not matter. Best regards, Wayne http://www.ncbi.nlm.nih.gov/blast /Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: Thank you Wayne. I tried with the sequence beginning immediately after "QUERY=", (called as bare sequence) but still I get the same error. The documentation on your URLAPI says that Query can have Accession(s), gi(S) or FASTA sequence. The format of the query for FASTA sequence is as shown: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA sequence, the query has description/definition followed by actual sequence. In that case, the format of my POST request match the requirement. Can you help me figure out why am I still getting error : "Cannot accept request, error code: -103" ? Attaching the log file having Query as bare sequence and FASTA sequence for your reference. Your help is much appreciated. Thanks, Sheetal On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten wrote: Hello, Our URLAPI, which your script should, but may or may not use, requires that the sequence begin immediately after "QUERY=". Your example shows a definition line preceding the sequence. You can get documentation on our URLAPI on this page (Web service interface): http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo Best regards, Wayne _~___~___~__~__~_~ Wayne Matten, PhD NCBI Public Services mattenw at mail.nih.gov On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: Hello, I am trying to use blastx program with 'nr' database in my Bioperl script remotely. While I do so, I get this error : Cannot accept request, error code: -103 The request that I send is : POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: bioperl-Bio_Tools_Run_ RemoteBlast/1.006001 Content-Length: 1945 Content-Type: application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx Can you please help me debug it. Thanks and Regards, Sheetal Thanks Sheetal On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields wrote: > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > chris > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > Adding some more details on OS and BioPerl version > > > > OS: > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 07:54:58 > > UTC 2010 i686 GNU/Linux > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > BioPerl Version : > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl -MBio::Root::Version > -e > > 'print $Bio::Root::Version::VERSION,"\n"' > > 1.006001 > > > > Attached is the error that I get while running the RemoteBlast. > > > > Thanks, > > Sheetal > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > wrote: > > > >> Hi, > >> > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > >> is the complete script : > >> #Remote-blast "factory object" creation and blast-parameter > >> initialization > >> > >> use Bio::Tools::Run::RemoteBlast; > >> use strict; > >> my $prog = 'blastx'; > >> my $db = 'nr/nt'; > >> my $e_val= '1e-10'; > >> > >> my @params = ( '-prog' => $prog, > >> '-data' => $db, > >> '-expect' => $e_val, > >> '-readmethod' => 'SearchIO' ); > >> > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > >> > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > >> > >> #$v is just to turn on and off the messages > >> my $v = 0; > >> > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > >> ); > >> > >> while (my $input = $str->next_seq()){ > >> #Blast a sequence against a database: > >> > >> #Alternatively, you could pass in a file with many > >> #sequences rather than loop through sequence one at a time > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > >> #and swap the two lines below for an example of that. > >> my $r = $factory->submit_blast($input); > >> #my $r = $factory->submit_blast('amino.fa'); > >> > >> print STDERR "waiting..." if( $v > 0 ); > >> while ( my @rids = $factory->each_rid ) { > >> foreach my $rid ( @rids ) { > >> my $rc = $factory->retrieve_blast($rid); > >> if( !ref($rc) ) { > >> if( $rc < 0 ) { > >> print "removing rid as rc is < 0"; > >> $factory->remove_rid($rid); > >> } > >> print STDERR "." if ( $v > 0 ); > >> sleep 5; > >> } else { > >> my $result = $rc->next_result(); > >> #save the output > >> print "saving to file"; > >> my $filename = "contig_236.out"; #$result->query_name()."\.out"; > >> $factory->save_output($filename); > >> $factory->remove_rid($rid); > >> print "\nQuery Name: ", $result->query_name(), "\n"; > >> while ( my $hit = $result->next_hit ) { > >> next unless ( $v > 0); > >> print "\thit name is ", $hit->name, "\n"; > >> while( my $hsp = $hit->next_hsp ) { > >> print "\t\tscore is ", $hsp->score, "\n"; > >> } > >> } > >> } > >> } > >> } > >> } > >> > >> But when I run this, I get an error in html format which says "Cannot > >> accept request, error code: -103". Attaching the error file for > reference. > >> Can you please help me with debugging this error? Your help is much > >> appreciated. > >> > >> Also, informing about the previous error that I fixed by adding this > line: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > >> I was getting prior to adding this line was : > >> --------------------- WARNING --------------------- > >> MSG:

An error has occurred on the > >> server, The server is unable to format right now, please try again in a > few > >> minutes. If the problem (Informational Message: No alias or index file > >> found for protein database [nr/nt] in search path > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > >> 4CF5MY9101P

> >> > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > >> > >> # 1) set your database like this: > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > >> > >> > >> # 2) add this line before submitting the job: > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > >> > >> I think it will be great if you can add this to the synopsis section of > >> RemoteBlast.pm > >> > >> Thanks, > >> Sheetal > >> > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From shachigahoimbi at gmail.com Fri Jul 23 11:01:01 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:31:01 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From shachigahoimbi at gmail.com Fri Jul 23 11:28:05 2010 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 23 Jul 2010 16:58:05 +0530 Subject: [Bioperl-l] bioperl modules Message-ID: I want to use following bioperl modules. I have installed bioperl 1.6.I. have searched all modules in it but i have not found following modules. I want to use it. please tell me if anyone know about these modules and use of it. temp- for temperature checking ac- for count of AC content gc- for count of GC content dimer- check bases for dimerization check 5- Check the presence of GC, CG, C or G at 5' check 3- Check the presence of GC, CG, C or G at 3' basepair- calculate % of GC hairpin- calculate hairpin structure delta- calculate delta G value for primer temp diff- check for temperature difference in left and right primer please tell me if anyone know about these modules. Thanks in advance -- Regards, Shachi From giles.weaver at bbsrc.ac.uk Fri Jul 23 11:31:11 2010 From: giles.weaver at bbsrc.ac.uk (Giles Weaver) Date: Fri, 23 Jul 2010 12:31:11 +0100 Subject: [Bioperl-l] bioperl modules In-Reply-To: References: Message-ID: <4C497D7F.1060806@bbsrc.ac.uk> See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. Regards, Giles On 23/07/10 12:01, Shachi Gahoi wrote: > I want to use following bioperl modules. I have installed bioperl 1.6.I. > have searched all modules in it but i have not found following modules. I > want to use it. please tell me if anyone know about these modules and use of > it. > > temp- for temperature checking > ac- for count of AC content > gc- for count of GC content > dimer- check bases for dimerization > check 5- Check the presence of GC, CG, C or G at 5' > check 3- Check the presence of GC, CG, C or G at 3' > basepair- calculate % of GC > hairpin- calculate hairpin structure > delta- calculate delta G value for primer > temp diff- check for temperature difference in left and right primer > > please tell me if anyone know about these modules. > > Thanks in advance > > > From cjfields at illinois.edu Fri Jul 23 13:17:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 08:17:41 -0500 Subject: [Bioperl-l] bioperl modules In-Reply-To: <4C497D7F.1060806@bbsrc.ac.uk> References: <4C497D7F.1060806@bbsrc.ac.uk> Message-ID: <688164AF-AF7B-49D0-9E68-A4916C7A2DDC@illinois.edu> This sounds suspiciously like homework, so I'm reluctant to give any direct answers. Most (all?) of these are covered in the Tisdall books, IIRC, and all use regexes or transliteration, that's about all I'll say. chris On Jul 23, 2010, at 6:31 AM, Giles Weaver wrote: > See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm calculation. > Most of the other checks are trivially easy in perl/bioperl, with the exception of checks for hairpin and dimer formation - I'd be interested to hear if anyone has implemented these checks. > > Regards, > > Giles > > On 23/07/10 12:01, Shachi Gahoi wrote: >> I want to use following bioperl modules. I have installed bioperl 1.6.I. >> have searched all modules in it but i have not found following modules. I >> want to use it. please tell me if anyone know about these modules and use of >> it. >> >> temp- for temperature checking >> ac- for count of AC content >> gc- for count of GC content >> dimer- check bases for dimerization >> check 5- Check the presence of GC, CG, C or G at 5' >> check 3- Check the presence of GC, CG, C or G at 3' >> basepair- calculate % of GC >> hairpin- calculate hairpin structure >> delta- calculate delta G value for primer >> temp diff- check for temperature difference in left and right primer >> >> please tell me if anyone know about these modules. >> >> Thanks in advance >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From pg4 at sanger.ac.uk Fri Jul 23 08:06:38 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 09:06:38 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' Message-ID: Hello, Regarding the recent post about installing bioperl as non root, http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique http://perl.jonallen.info/writing/articles/install-perl-modules-without-root I wanted to put it in the talk page first, but there is an 'issue': The talk link points to http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix Talk:Installing Bioperl for Unix 2 and in this talk page, the page link point to a deleted page http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 Editing Installing Bioperl for Unix 2 Warning: You are recreating a page that was previously deleted. You should consider whether it is appropriate to continue editing this page. The deletion log for this page is provided here for convenience: * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing Bioperl for Unix 2" ? (testing out page (adding back from file)) Just to let you know. ----- Pablo Marin-Garcia -- 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 Fri Jul 23 15:07:23 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 10:07:23 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: Message-ID: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Pablo, No idea how that happened, but I removed the older discussion page and my obsolete comment, along with the redirect on the main discussion page. Edit away! chris On Jul 23, 2010, at 3:06 AM, Pablo Marin-Garcia wrote: > Hello, > > Regarding the recent post about installing bioperl as non root, > > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > I wanted to update the wiki page puting a note about local::lib and the bootstraping technique for your local installs. > > http://search.cpan.org/~getty/local-lib-1.006005/lib/local/lib.pm#The_bootstrapping_technique > http://perl.jonallen.info/writing/articles/install-perl-modules-without-root > > I wanted to put it in the talk page first, but there is an 'issue': > > The talk link points to > http://www.bioperl.org/wiki/Talk:Installing_Bioperl_for_Unix > Talk:Installing Bioperl for Unix 2 > > and in this talk page, the page link point to a deleted page > http://www.bioperl.org/w/index.php?title=Installing_Bioperl_for_Unix_2&action=edit&redlink=1 > > Editing Installing Bioperl for Unix 2 > Warning: You are recreating a page that was previously deleted. > > You should consider whether it is appropriate to continue editing this page. > The deletion log for this page is provided here for convenience: > > * 13:11, 13 June 2006 Cjfields (Talk | contribs) deleted "Installing > Bioperl > for Unix 2" ? (testing out page (adding back from file)) > > > Just to let you know. > > ----- > > Pablo Marin-Garcia > > > > -- > 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. > _______________________________________________ > 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 Fri Jul 23 15:42:09 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 09:42:09 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: Thanks for that addition to the wiki, Pablo! Much appreciated. I did not know about local::lib. Dave From pg4 at sanger.ac.uk Fri Jul 23 16:52:03 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 17:52:03 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Dave Messina wrote: > Thanks for that addition to the wiki, Pablo! Much appreciated. > > I did not know about local::lib. > [This is a bit off-topic but probably useful for core developers] Then probably you don't know about App::perlbrew Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ---- Copied from the SYNOPSIS: # Initialize perlbrew init # Install some Perls perlbrew install perl-5.8.1 perlbrew install perl-5.11.5 # See what were installed perlbrew installed # Switch perl in the $PATH perlbrew switch perl-5.11.5 perl -v # Switch to another version perlbrew switch perl-5.8.1 perl -v # Switch to a certain perl executable not managed by perlbrew. perlbrew switch /usr/bin/perl # Or turn it off completely. Useful when you messed up too deep. perlbrew off # Use 'switch' command to turn it back on. perlbrew switch perl-5.11.5 -Pablo > > Dave > ----- Pablo Marin-Garcia -- 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 Fri Jul 23 16:57:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 11:57:05 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ... yes, just started using this myself. Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. chris From cjfields at illinois.edu Fri Jul 23 17:01:20 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:01:20 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> Message-ID: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > On Fri, 23 Jul 2010, Dave Messina wrote: > >> Thanks for that addition to the wiki, Pablo! Much appreciated. >> >> I did not know about local::lib. >> > > [This is a bit off-topic but probably useful for core developers] > Then probably you don't know about > > App::perlbrew > > Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. ...and completely forgot to mention the tremendous benefits of App::perlbrew for development! Lots of very nice tools becoming available these days... chris From cjfields at illinois.edu Fri Jul 23 17:20:44 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:20:44 -0500 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> http://github.com/cjfields/bioperl6 http://github.com/cjfields/biome :) chris On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > > extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: > > http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html > > I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. > > > Have a good weekend > > -Pablo > > > > On Fri, 23 Jul 2010, Chris Fields wrote: > >> >> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >> >>> On Fri, 23 Jul 2010, Dave Messina wrote: >>> >>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>> >>>> I did not know about local::lib. >>>> >>> >>> [This is a bit off-topic but probably useful for core developers] >>> Then probably you don't know about >>> >>> App::perlbrew >>> >>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >> ... >> >> yes, just started using this myself. >> >> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >> >> chris > > > ----- > > Pablo Marin-Garcia > > > > -- > 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 sheetu.piscean at gmail.com Fri Jul 23 17:04:59 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 10:04:59 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: I did remove that line but doesn't help. I still keep getting this error: MSG:

An error has occurred on the server, The server is unable to format right now, please try again in a few minutes. If the problem (Informational Message: No alias or index file found for protein database [nr/nt] in search path [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4KJE1YJ601N

Any pointers ?? - Sheetal On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > This is set via '-prog' parameter. > > chris > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to Blast-help as well > and they have to say that "there is something wrong with the URL, didn't > give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default it is set to > plain, I guess this value is for standard blast pgm. like blastp, blastx, > etc) gives me this error : > > An error has occurred on the server, The server is unable to format right > now, please try again in a few minutes. If the problem (Informational > Message: No alias or index file found for protein database [nr/nt] in search > path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for debugging further > : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some errors. The > URL below works; note that order of parameters does not matter. > > > > Best regards, > > Wayne > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=%3EContig_236+%0A%0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning immediately after > "QUERY=", (called as bare sequence) but still I get the same error. > > > > The documentation on your URLAPI says that Query can have Accession(s), > gi(S) or FASTA sequence. The format of the query for FASTA sequence is as > shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus for FASTA > sequence, the query has description/definition followed by actual sequence. > In that case, the format of my POST request match the requirement. > > > > Can you help me figure out why am I still getting error : "Cannot accept > request, error code: -103" ? Attaching the log file having Query as bare > sequence and FASTA sequence for your reference. Your help is much > appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not use, requires > that the sequence begin immediately after "QUERY=". Your example shows a > definition line preceding the sequence. You can get documentation on our > URLAPI on this page (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my Bioperl script > remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded > DATABASE=nr%2Fnt&QUERY=%3EContig_236+%0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI server, not > problems with the script. Is this still occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 > 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on 'nr' database. > Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , -format => > 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a time > > >> #Remove the loop starting 'while (my $input = $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; > #$result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which says "Cannot > > >> accept request, error code: -103". Attaching the error file for > reference. > > >> Can you please help me with debugging this error? Your help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by adding this > line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; The error > that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has occurred on > the > > >> server, The server is unable to format right now, please try again in > a few > > >> minutes. If the problem (Informational Message: No alias or index > file > > >> found for protein database [nr/nt] in search path > > >> [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the synopsis section > of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > From pg4 at sanger.ac.uk Fri Jul 23 17:17:50 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:17:50 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> Message-ID: extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. Have a good weekend -Pablo On Fri, 23 Jul 2010, Chris Fields wrote: > > On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: > >> On Fri, 23 Jul 2010, Dave Messina wrote: >> >>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>> >>> I did not know about local::lib. >>> >> >> [This is a bit off-topic but probably useful for core developers] >> Then probably you don't know about >> >> App::perlbrew >> >> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. > ... > > yes, just started using this myself. > > Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. > > chris ----- Pablo Marin-Garcia -- 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 Fri Jul 23 17:36:40 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 12:36:40 -0500 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: References: Message-ID: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> I've attached the code and example data that worked. This is using the latest bioperl on github, so maybe it's the version you have installed? chris On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > I did remove that line but doesn't help. I still keep getting this > error: > MSG:

An error has occurred on > the server, The server is unable to format right now, please try again > in a few minutes. If the problem (Informational Message: No alias or > index file found for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > 4KJE1YJ601N

> > Any pointers ?? > > - Sheetal > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > wrote: > Removing this line from your original script worked for me: > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > This is set via '-prog' parameter. > > chris > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > Yes the error is still occurring. I have emailed to > Blast-help as well and they have to say that "there is > something wrong with the URL, didn't give any specifics". > > > > Also changing the parameter SERVICE to 'plain' (by default > it is set to plain, I guess this value is for standard blast > pgm. like blastp, blastx, etc) gives me this error : > > An error has occurred on the server, The server is unable to > format right now, please try again in a few minutes. If the > problem (Informational Message: No alias or index file found > for protein database [nr/nt] in search path > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I have sent an email today to blast-help for this error. > > > > Adding below the email conversation with blast-help for > debugging further : > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > wrote: > > Sheetal, > > > > You are right about the query syntax, but your URL has some > errors. The URL below works; note that order of parameters > does not matter. > > > > Best regards, > > Wayne > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > 3EContig_236+%0A% > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > Thank you Wayne. I tried with the sequence beginning > immediately after "QUERY=", (called as bare sequence) but > still I get the same error. > > > > The documentation on your URLAPI says that Query can have > Accession(s), gi(S) or FASTA sequence. The format of the query > for FASTA sequence is as shown: > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > for FASTA sequence, the query has description/definition > followed by actual sequence. In that case, the format of my > POST request match the requirement. > > > > Can you help me figure out why am I still getting error : > "Cannot accept request, error code: -103" ? Attaching the log > file having Query as bare sequence and FASTA sequence for your > reference. Your help is much appreciated. > > > > Thanks, > > Sheetal > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > wrote: > > Hello, > > > > Our URLAPI, which your script should, but may or may not > use, requires that the sequence begin immediately after > "QUERY=". Your example shows a definition line preceding the > sequence. You can get documentation on our URLAPI on this page > (Web service interface): > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > Best regards, > > Wayne > > > > _~___~___~__~__~_~ > > Wayne Matten, PhD > > NCBI Public Services > > mattenw at mail.nih.gov > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > Hello, > > > > I am trying to use blastx program with 'nr' database in my > Bioperl script remotely. While I do so, I get this error : > > Cannot accept request, error code: -103 > > > > The request that I send is : > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > bioperl-Bio_Tools_Run_ > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > 3EContig_236+% > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > >> > >> Can you please help me debug it. > >> > >> Thanks and Regards, > >> Sheetal > > > > Thanks > > Sheetal > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > wrote: > > The errors reported seem to indicate problems on the NCBI > server, not problems with the script. Is this still > occurring? > > > > chris > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > Adding some more details on OS and BioPerl version > > > > > > OS: > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > Jun 11 07:54:58 > > > UTC 2010 i686 GNU/Linux > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > BioPerl Version : > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > -MBio::Root::Version -e > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > 1.006001 > > > > > > Attached is the error that I get while running the > RemoteBlast. > > > > > > Thanks, > > > Sheetal > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > wrote: > > > > > >> Hi, > > >> > > >> I am trying to run RemoteBlast to blastx sequences on > 'nr' database. Here > > >> is the complete script : > > >> #Remote-blast "factory object" creation and > blast-parameter > > >> initialization > > >> > > >> use Bio::Tools::Run::RemoteBlast; > > >> use strict; > > >> my $prog = 'blastx'; > > >> my $db = 'nr/nt'; > > >> my $e_val= '1e-10'; > > >> > > >> my @params = ( '-prog' => $prog, > > >> '-data' => $db, > > >> '-expect' => $e_val, > > >> '-readmethod' => 'SearchIO' ); > > >> > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > >> > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; > > >> > > >> #$v is just to turn on and off the messages > > >> my $v = 0; > > >> > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > -format => 'fasta' > > >> ); > > >> > > >> while (my $input = $str->next_seq()){ > > >> #Blast a sequence against a database: > > >> > > >> #Alternatively, you could pass in a file with many > > >> #sequences rather than loop through sequence one at a > time > > >> #Remove the loop starting 'while (my $input = > $str->next_seq())' > > >> #and swap the two lines below for an example of that. > > >> my $r = $factory->submit_blast($input); > > >> #my $r = $factory->submit_blast('amino.fa'); > > >> > > >> print STDERR "waiting..." if( $v > 0 ); > > >> while ( my @rids = $factory->each_rid ) { > > >> foreach my $rid ( @rids ) { > > >> my $rc = $factory->retrieve_blast($rid); > > >> if( !ref($rc) ) { > > >> if( $rc < 0 ) { > > >> print "removing rid as rc is < 0"; > > >> $factory->remove_rid($rid); > > >> } > > >> print STDERR "." if ( $v > 0 ); > > >> sleep 5; > > >> } else { > > >> my $result = $rc->next_result(); > > >> #save the output > > >> print "saving to file"; > > >> my $filename = "contig_236.out"; # > $result->query_name()."\.out"; > > >> $factory->save_output($filename); > > >> $factory->remove_rid($rid); > > >> print "\nQuery Name: ", $result->query_name(), > "\n"; > > >> while ( my $hit = $result->next_hit ) { > > >> next unless ( $v > 0); > > >> print "\thit name is ", $hit->name, "\n"; > > >> while( my $hsp = $hit->next_hsp ) { > > >> print "\t\tscore is ", $hsp->score, "\n"; > > >> } > > >> } > > >> } > > >> } > > >> } > > >> } > > >> > > >> But when I run this, I get an error in html format which > says "Cannot > > >> accept request, error code: -103". Attaching the error > file for reference. > > >> Can you please help me with debugging this error? Your > help is much > > >> appreciated. > > >> > > >> Also, informing about the previous error that I fixed by > adding this line: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'blastx'; The error that > > >> I was getting prior to adding this line was : > > >> --------------------- WARNING --------------------- > > >> MSG:

An error has > occurred on the > > >> server, The server is unable to format right now, please > try again in a few > > >> minutes. If the problem (Informational Message: No > alias or index file > > >> found for protein database [nr/nt] in search path > > >> > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > RID: > > >> 4CF5MY9101P

> > >> > > >> It kinda took me a while to find out the 2 > requirements > > >> > > >> # 1) set your database like this: > > >> -database => 'cdsearch/cdd', # c.f. > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options > > >> > > >> > > >> # 2) add this line before submitting the job: > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > 'rpsblast'; > > >> > > >> I think it will be great if you can add this to the > synopsis section of > > >> RemoteBlast.pm > > >> > > >> Thanks, > > >> Sheetal > > >> > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: test.pl Type: application/x-perl Size: 2211 bytes Desc: not available URL: -------------- next part -------------- >Foo My description here AATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGG CGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGA GGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCT CCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCC ACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAG AAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCAT GGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAAT GCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCC TGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCG GGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGA TTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGC CCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAG CCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAAT CCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGG CTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTAT ACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCT CAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGC GCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACG CAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTG TCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTC AGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGAT GAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTG CGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCAC GCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGA GACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACT CAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCA TCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAAC AGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAG CGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTT CTGT From pg4 at sanger.ac.uk Fri Jul 23 17:33:10 2010 From: pg4 at sanger.ac.uk (Pablo Marin-Garcia) Date: Fri, 23 Jul 2010 18:33:10 +0100 (BST) Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <94269571-BAE2-4DF4-A265-25EE4A0456AF@illinois.edu> <09F74919-258E-40AC-A436-6A894BCC6004@illinois.edu> Message-ID: On Fri, 23 Jul 2010, Chris Fields wrote: > http://github.com/cjfields/bioperl6 oh, very nice!. > http://github.com/cjfields/biome one of my to-do things for my holidays is to git clone it and star to play with it. I have several mOOse modules for GWAS that I am going to release soon but I would like to accomodate them first to the bioperl look and feel. > :) > > chris > > On Jul 23, 2010, at 12:17 PM, Pablo Marin-Garcia wrote: > >> >> extending a bit more this off topic thread about nice perl modern tools, just mention for the adventurous that you would be able, next month, to test porting some bioperl to perl6 if you wish: >> >> http://pablomarin-garcia.blogspot.com/2010/07/perl-rakudo-start-will-be-available-at.html >> >> I have not tried the inline-Rakudo yet but seems a nice way of start to test perl6 inside your perl5. >> >> >> Have a good weekend >> >> -Pablo >> >> >> >> On Fri, 23 Jul 2010, Chris Fields wrote: >> >>> >>> On Jul 23, 2010, at 11:52 AM, Pablo Marin-Garcia wrote: >>> >>>> On Fri, 23 Jul 2010, Dave Messina wrote: >>>> >>>>> Thanks for that addition to the wiki, Pablo! Much appreciated. >>>>> >>>>> I did not know about local::lib. >>>>> >>>> >>>> [This is a bit off-topic but probably useful for core developers] >>>> Then probably you don't know about >>>> >>>> App::perlbrew >>>> >>>> Very useful when you want to test your api in different perl versions, or now that perl is releasing new versions more frequently you can test the latest one, easily. >>> ... >>> >>> yes, just started using this myself. >>> >>> Re: local::lib, I don't use it much, but I have found perl 5.12 is a bit easier when installing modules locally. In fact, will probably install perl and modules locally from now on instead of going through the hassle of dealing with sysadmins. >>> >>> chris >> >> >> ----- >> >> Pablo Marin-Garcia >> >> >> >> -- >> 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. > > ----- Pablo Marin-Garcia -- 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 sheetu.piscean at gmail.com Fri Jul 23 18:15:51 2010 From: sheetu.piscean at gmail.com (sheetal gosrani) Date: Fri, 23 Jul 2010 11:15:51 -0700 Subject: [Bioperl-l] Regarding RemoteBlast: Getting error "Cannot accept request, error code: -103" In-Reply-To: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> References: <1279906600.27442.7.camel@pyrimidine.igb.uiuc.edu> Message-ID: Thanks a lot Chris. It worked for me as well :) - Sheetal On Fri, Jul 23, 2010 at 10:36 AM, Chris Fields wrote: > I've attached the code and example data that worked. This is using the > latest bioperl on github, so maybe it's the version you have installed? > > chris > > On Fri, 2010-07-23 at 10:04 -0700, sheetal gosrani wrote: > > I did remove that line but doesn't help. I still keep getting this > > error: > > MSG:

An error has occurred on > > the server, The server is unable to format right now, please try again > > in a few minutes. If the problem (Informational Message: No alias or > > index file found for protein database [nr/nt] in search path > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) > > persists - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: > > 4KJE1YJ601N

> > > > Any pointers ?? > > > > - Sheetal > > > > On Thu, Jul 22, 2010 at 6:52 PM, Chris Fields > > wrote: > > Removing this line from your original script worked for me: > > > > $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'blastx'; > > > > > > This is set via '-prog' parameter. > > > > chris > > > > > > On Jul 22, 2010, at 7:30 PM, sheetal gosrani wrote: > > > > > Yes the error is still occurring. I have emailed to > > Blast-help as well and they have to say that "there is > > something wrong with the URL, didn't give any specifics". > > > > > > Also changing the parameter SERVICE to 'plain' (by default > > it is set to plain, I guess this value is for standard blast > > pgm. like blastp, blastx, etc) gives me this error : > > > An error has occurred on the server, The server is unable to > > format right now, please try again in a few minutes. If the > > problem (Informational Message: No alias or index file found > > for protein database [nr/nt] in search path > > > [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]) persists > - Contact Blast-help at ncbi.nlm.nih.gov and include your RID: 4H2Y96KZ012 I > have sent an email today to blast-help for this error. > > > > > > Adding below the email conversation with blast-help for > > debugging further : > > > On Thu, Jul 22, 2010 at 6:20 AM, Wayne Matten > > wrote: > > > Sheetal, > > > > > > You are right about the query syntax, but your URL has some > > errors. The URL below works; note that order of parameters > > does not matter. > > > > > > Best regards, > > > Wayne > > > > > > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=% > > 3EContig_236+%0A% > > > 0DAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&DATABASE=nr&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&CMD=Put&FILTER=L&PROGRAM=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&DESCRIPTIONS=100&FORMAT_TYPE=Text > > > > > > On Jul 21, 2010, at 2:57 PM, sheetal gosrani wrote: > > > > > > Thank you Wayne. I tried with the sequence beginning > > immediately after "QUERY=", (called as bare sequence) but > > still I get the same error. > > > > > > The documentation on your URLAPI says that Query can have > > Accession(s), gi(S) or FASTA sequence. The format of the query > > for FASTA sequence is as shown: > > > http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml Thus > > for FASTA sequence, the query has description/definition > > followed by actual sequence. In that case, the format of my > > POST request match the requirement. > > > > > > Can you help me figure out why am I still getting error : > > "Cannot accept request, error code: -103" ? Attaching the log > > file having Query as bare sequence and FASTA sequence for your > > reference. Your help is much appreciated. > > > > > > Thanks, > > > Sheetal > > > > > > On Wed, Jul 21, 2010 at 7:45 AM, Wayne Matten > > wrote: > > > Hello, > > > > > > Our URLAPI, which your script should, but may or may not > > use, requires that the sequence begin immediately after > > "QUERY=". Your example shows a definition line preceding the > > sequence. You can get documentation on our URLAPI on this page > > (Web service interface): > > > > > > > > > http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo > > > > > > Best regards, > > > Wayne > > > > > > _~___~___~__~__~_~ > > > Wayne Matten, PhD > > > NCBI Public Services > > > mattenw at mail.nih.gov > > > > > > > > > On Jul 20, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > Hello, > > > > > > I am trying to use blastx program with 'nr' database in my > > Bioperl script remotely. While I do so, I get this error : > > > Cannot accept request, error code: -103 > > > > > > The request that I send is : > > > POST http://blast.ncbi.nlm.nih.gov/Blast.cgi User-Agent: > > bioperl-Bio_Tools_Run_ > > >> RemoteBlast/1.006001 Content-Length: 1945 Content-Type: > > application/x-www-form-urlencoded DATABASE=nr%2Fnt&QUERY=% > > 3EContig_236+% > > > 0AAATCTGTTCCTGTTTTTTGAGCCCCTGGCGGGCAAACGGCATGTCCAGGTCAGCGAGCGGCGCACGAAGGTGGATTGGGCCCACGCCATGCGTCATCTGGCCGATGAACTGTACCCAGAGGCAGACGTGATCGTTGTGGTGATGGACAATCTGAACCCGCACAGCCCGGCTTCCTTCTCCGAGGCATTCGAGCCCGCCGAGGCGCAACGGCTCCGAGCACGCTTCGCGTTCCACTCCACGCCCAAGCACGGCAGTTGGCTGAATATGGCCGAGATTGAATTGCGTGCCTTGGTGAGAAGCTGCCTGAATCGCCGGATTCCAGACCAGGCCACCCTGCATCGGGAGGTCCAGGCATGGGTGGAGGAGCGGAACCAAAAAGCCGTCCGAGTAGACTGGCGTTTCACCACCGCCAATGCCCGCATGAAACTGAAACATTTGTATCCAAAGATTCATGCTTGACAGAGTACTAGaCCTGACCAAACTGGaKCWWCaSCWTTCCATATCCGAGGGCTTCAGTCCGACGGCTCGCGCGGGATAGCGGATTTAATGCTCAATCTCCATCGAGCCCGACGGCTCGTGCGGGATAGCGGATTATAGCGGTTCTCAGATACGTTGACTCCTGTCCGGGTCTGCCGTGTCGTGCGAGGCGCCCGTTTCCGCCACGCGCTCAGGGAGGGCTTATGGTCTTTGAGTAAATAATCCGCCATAGCCCGCGCAGGCGGGCTTTGCATTCCATAGCCGCGGGCTTATGGTCTTTGAATAAATAATCCGCTACAGCCCGCGCAGGCGGGCTTCGCCTTGGCTAGCCGAGGGCTTCAGCCCCACGGCTAGCGCGGGATAGCAGAATAAATTCTCAATCTCCATTAGCCCCACGGCAAGGGCGTATACCGGATTTATTTCTCAATCTCCATCAGCCCGCACGCGCGGAGTCGCGCCCGCAGTTCTCAGATGCGTTGACCCTTGTCCGGGTCTGCTGTGTCGCACAAGGCGCCCGCTTCCGCTGCGCTCCCCATCTCCGCGCCTCCTCGCCTCCGCGTGAGCCGGTCTGATGCATGCGGAGACGCAGAGCACACGGAGAGATGGCGCACAAGGCGTCTGCTTTCGCTGGCGTGTTCaAcCCTGTCCAACAAGACCAATATTTAGTGAGAACTGCTATATTTCTCACATATATCGGCAGCGTCAGCGAAGCGGTGATTGTGCAGACGGACGCTGCCGGACGACCGCAGGCGCTGGTAACGATGAGCCGGTCGGGTATTGCGCCTGGGTTTGTAACGCGCGGCGAACCCGGTCTGCTTCTTGCGGCAACAGYGTGTCCACCTGTGTCTGCAAAGCTCGACGAACGCTGTCACTCCCTTCACGCAGCCaatAAtcgTATATCTGTTTCTTCAACGCTTGACGAACTTTATCCTCTTCTTGAGACAGGAACTCGTTCACCCGGCTTTGCAACGCATGGCGAACGTCGCTTTCCGCCTGACTCAGCTGACTCTTTACCCGATCTTGCAACGCCGCGCGGAATTGGCTTTCCGTTTGACGCATCAAATCATTCATCTTTGCCTGGAACGCCTGGAGCCATTCACTCTTTACTTGATCCAACAGCTCTGCAGCGTGATTCTGCAATGTCTCGTGAACCCGGTCTTGCTCTTGCTCCAGTAGCGCTGCAACCTGGGTCTGTAATGCGCTGCGGACGTCACCCTTCTCTTGACGTACCAGTTCTGT&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=blastx&ALIGNMENTS=50&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&DESCRIPTIONS=100&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&PROGRAM=blastx > > >> > > >> Can you please help me debug it. > > >> > > >> Thanks and Regards, > > >> Sheetal > > > > > > Thanks > > > Sheetal > > > > > > On Thu, Jul 22, 2010 at 4:54 PM, Chris Fields > > wrote: > > > The errors reported seem to indicate problems on the NCBI > > server, not problems with the script. Is this still > > occurring? > > > > > > chris > > > > > > On Jul 21, 2010, at 4:49 PM, sheetal gosrani wrote: > > > > > > > Adding some more details on OS and BioPerl version > > > > > > > > OS: > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ uname -a > > > > Linux sheetal-ubuntu 2.6.32-23-generic #37-Ubuntu SMP Fri > > Jun 11 07:54:58 > > > > UTC 2010 i686 GNU/Linux > > > > > > > > Perl : v5.10.1 (*) built for i486-linux-gnu-thread-multi > > > > > > > > BioPerl Version : > > > > sheetal at sheetal-ubuntu:~/Setups/BioPerl-1.6.1$ perl > > -MBio::Root::Version -e > > > > 'print $Bio::Root::Version::VERSION,"\n"' > > > > 1.006001 > > > > > > > > Attached is the error that I get while running the > > RemoteBlast. > > > > > > > > Thanks, > > > > Sheetal > > > > > > > > On Tue, Jul 20, 2010 at 5:30 PM, sheetal gosrani > > > > wrote: > > > > > > > >> Hi, > > > >> > > > >> I am trying to run RemoteBlast to blastx sequences on > > 'nr' database. Here > > > >> is the complete script : > > > >> #Remote-blast "factory object" creation and > > blast-parameter > > > >> initialization > > > >> > > > >> use Bio::Tools::Run::RemoteBlast; > > > >> use strict; > > > >> my $prog = 'blastx'; > > > >> my $db = 'nr/nt'; > > > >> my $e_val= '1e-10'; > > > >> > > > >> my @params = ( '-prog' => $prog, > > > >> '-data' => $db, > > > >> '-expect' => $e_val, > > > >> '-readmethod' => 'SearchIO' ); > > > >> > > > >> my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > > >> > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; > > > >> > > > >> #$v is just to turn on and off the messages > > > >> my $v = 0; > > > >> > > > >> my $str = Bio::SeqIO->new(-file=>'davcg_small.fasta' , > > -format => 'fasta' > > > >> ); > > > >> > > > >> while (my $input = $str->next_seq()){ > > > >> #Blast a sequence against a database: > > > >> > > > >> #Alternatively, you could pass in a file with many > > > >> #sequences rather than loop through sequence one at a > > time > > > >> #Remove the loop starting 'while (my $input = > > $str->next_seq())' > > > >> #and swap the two lines below for an example of that. > > > >> my $r = $factory->submit_blast($input); > > > >> #my $r = $factory->submit_blast('amino.fa'); > > > >> > > > >> print STDERR "waiting..." if( $v > 0 ); > > > >> while ( my @rids = $factory->each_rid ) { > > > >> foreach my $rid ( @rids ) { > > > >> my $rc = $factory->retrieve_blast($rid); > > > >> if( !ref($rc) ) { > > > >> if( $rc < 0 ) { > > > >> print "removing rid as rc is < 0"; > > > >> $factory->remove_rid($rid); > > > >> } > > > >> print STDERR "." if ( $v > 0 ); > > > >> sleep 5; > > > >> } else { > > > >> my $result = $rc->next_result(); > > > >> #save the output > > > >> print "saving to file"; > > > >> my $filename = "contig_236.out"; # > > $result->query_name()."\.out"; > > > >> $factory->save_output($filename); > > > >> $factory->remove_rid($rid); > > > >> print "\nQuery Name: ", $result->query_name(), > > "\n"; > > > >> while ( my $hit = $result->next_hit ) { > > > >> next unless ( $v > 0); > > > >> print "\thit name is ", $hit->name, "\n"; > > > >> while( my $hsp = $hit->next_hsp ) { > > > >> print "\t\tscore is ", $hsp->score, "\n"; > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> } > > > >> > > > >> But when I run this, I get an error in html format which > > says "Cannot > > > >> accept request, error code: -103". Attaching the error > > file for reference. > > > >> Can you please help me with debugging this error? Your > > help is much > > > >> appreciated. > > > >> > > > >> Also, informing about the previous error that I fixed by > > adding this line: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'blastx'; The error that > > > >> I was getting prior to adding this line was : > > > >> --------------------- WARNING --------------------- > > > >> MSG:

An error has > > occurred on the > > > >> server, The server is unable to format right now, please > > try again in a few > > > >> minutes. If the problem (Informational Message: No > > alias or index file > > > >> found for protein database [nr/nt] in search path > > > >> > > > [/export/home/splitd/blastdb/blast0:/blast/db/disk.blast/blast1::]) persists > > > >> - Contact Blast-help at ncbi.nlm.nih.gov and include your > > RID: > > > >> 4CF5MY9101P

> > > >> > > > >> It kinda took me a while to find out the 2 > > requirements< > http://www.bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast> > > > >> > > > >> # 1) set your database like this: > > > >> -database => 'cdsearch/cdd', # c.f. > > > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for > other cdd database options > > > >> > > > >> > > > >> # 2) add this line before submitting the job: > > > >> $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = > > 'rpsblast'; > > > >> > > > >> I think it will be great if you can add this to the > > synopsis section of > > > >> RemoteBlast.pm > > > >> > > > >> Thanks, > > > >> Sheetal > > > >> > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > From y-bushmanova at northwestern.edu Fri Jul 23 18:54:19 2010 From: y-bushmanova at northwestern.edu (Yulia Bushmanova) Date: Fri, 23 Jul 2010 13:54:19 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E26F.4020103@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> Message-ID: <4C49E55B.6000509@northwestern.edu> Sorry, first email had wrong file attached Yulia Yulia Bushmanova wrote: > Hi All, > > I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and > got following error: > > not well-formed (invalid token) at line 32, column 48, byte 3095 at > /usr/lib/perl5/XML/Parser.pm line 187 > > Looks like parser complains on the copyright sign, if I manually > remove it from file parsing goes fine. XML::Parser is version 2.36. > > Any ideas on how to deal with this error? > > Thanks in advance, > Yulia -------------- next part -------------- A non-text attachment was scrubbed... Name: allRefs_07232010.xml Type: text/xml Size: 42911 bytes Desc: not available URL: From David.Messina at sbc.su.se Fri Jul 23 19:00:07 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 23 Jul 2010 13:00:07 -0600 Subject: [Bioperl-l] bioperl wiki oddity for 'installing bioperl in unix' In-Reply-To: <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> References: <2DFEF5B0-64D4-429D-89C2-8C11ABED0880@illinois.edu> <2A2855BD-523B-4CDF-9B8F-42F48655677D@illinois.edu> Message-ID: <9C35A675-7A6C-4A33-8826-443CD4E5E541@sbc.su.se> Cool, thanks for the pointer to perlbrew! Dave From cjfields at illinois.edu Fri Jul 23 19:08:03 2010 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jul 2010 14:08:03 -0500 Subject: [Bioperl-l] Bio::Biblio::IO copyright parsing In-Reply-To: <4C49E55B.6000509@northwestern.edu> References: <4C49E26F.4020103@northwestern.edu> <4C49E55B.6000509@northwestern.edu> Message-ID: <105D6D53-1465-44ED-BA6A-B2D642F09BA9@illinois.edu> You should file this as a bug, along with the output. My guess is it has to do with character encoding, but not sure. chris On Jul 23, 2010, at 1:54 PM, Yulia Bushmanova wrote: > Sorry, first email had wrong file attached > > Yulia > > Yulia Bushmanova wrote: >> Hi All, >> >> I was trying to parse Pubmed xml with Bio::Biblio::IO (v.1.006001) and got following error: >> >> not well-formed (invalid token) at line 32, column 48, byte 3095 at /usr/lib/perl5/XML/Parser.pm line 187 >> >> Looks like parser complains on the copyright sign, if I manually remove it from file parsing goes fine. XML::Parser is version 2.36. >> >> Any ideas on how to deal with this error? >> >> Thanks in advance, >> Yulia > > > > > > > 20643054 > > 2010 > 7 > 20 > >
> > 1542-0086 > > 99 > 2 > > 2010 > Jul > 21 > > > Biophysical journal > > Bimodal Analysis Reveals a General Scaling Law Governing Nondirected and Chemotactic Cell Motility. > > 367-376 > > > Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a nondirected fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses. Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multiscale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both nondirected and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines, indicating that the coupling of reorientation and persistence holds across species and making it possible to describe the complexity of cell motility in a surprisingly general and simple manner. With this new perspective, we analyzed the motility of Dictyostelium mutants, and found four in which the coupling between two modes was altered. Our results point to a fundamental underlying principle, described by a simple scaling law, unifying mechanisms of eukaryotic cell motility at several scales. > Copyright ? 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. > > Department of Pharmacology, Vanderbilt University, Nashville, Tennessee. > > > Gruver > J Scott > JS > > > Potdar > Alka A > AA > > > Jeon > Junhwan > J > > > Sai > Jiqing > J > > > Anderson > Bridget > B > > > Webb > Donna > D > > > Richmond > Ann > A > > > Quaranta > Vito > V > > > Cummings > Peter T > PT > > > Chung > Chang Y > CY > > > ENG > > JOURNAL ARTICLE > >
> > Biophys J > 0370626 > 0006-3495 > > > > > > 2009 > 12 > 17 > > > 2010 > 3 > 9 > > > 2010 > 3 > 11 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > 2010 > 7 > 21 > 6 > 0 > > > ppublish > > S0006-3495(10)00710-1 > 10.1016/j.bpj.2010.03.073 > 20643054 > > > > > > > > 20640912 > > 2010 > 7 > 19 > >
> > 1420-9071 > > > 2010 > Jul > 18 > > > Cellular and molecular life sciences : CMLS > > Redundant and unique roles of coronin proteins in Dictyostelium. > > > > > Dictyostelium discoideum harbors a short (CRN12) and a long coronin (CRN7) composed of one and two beta-propellers, respectively. They are primarily present in the cell cortex and cells lacking CRN12 (corA (-)) or CRN7 (corB (-)) have defects in actin driven processes. We compared the characteristics of a mutant cell line (corA (-) /corB (-)) lacking CRN12 and CRN7 with the single mutants focusing on cytokinesis, phagocytosis, chemotaxis and development. Cytokinesis, uptake of small particles, and developmental defects were not enhanced in the corA (-) /corB (-) strain as compared to the single mutants, whereas motility and phagocytosis of yeast particles were more severely impaired. It appears that although both proteins affect the same processes they do not act in a redundant manner. Rather, they often act antagonistically, which is in accordance with their proposed roles in the actin cytoskeleton where CRN12 acts in actin disassembly whereas CRN7 stabilizes actin filaments and protects them from disassembly. > > Institute for Biochemistry I, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931, Cologne, Germany. > > > Shina > Maria C > MC > > > M?ller-Taubenberger > Annette > A > > > Unal > Can > C > > > Schleicher > Michael > M > > > Steinert > Michael > M > > > Eichinger > Ludwig > L > > > M?ller > Rolf > R > > > Blau-Wasser > Rosemarie > R > > > Gl?ckner > Gernot > G > > > Noegel > Angelika A > AA > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 18 > >
> > Cell Mol Life Sci > 9705402 > 1420-682X > > > > > > 2010 > 2 > 3 > > > 2010 > 7 > 5 > > > 2010 > 5 > 23 > > > 2010 > 7 > 18 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 10.1007/s00018-010-0455-y > 20640912 > > > > > > > > 20639697 > > 2010 > 7 > 19 > >
> > 1554-8635 > > 6 > 6 > > 2010 > Aug > 22 > > > Autophagy > > A second signal for autophagic cell death? > > > > > Dictyostelium cells in monolayers in vitro lend themselves well to a study of autophagic cell death (ACD). There is no apoptosis machinery in the protist Dictyostelium, no caspase nor Bcl-2 family members (except a paracaspase whose inactivation does not alter cell death), thus there is no apoptosis that could interfere with, or substitute for, nonapoptotic cell death. Also, Dictyostelium, a eukaryote, has a haploid genome, which facilitates random insertional mutagenesis. > > Centre d'Immunologie de Marseille-Luminy, Facult? des Sciences de Luminy, Aix Marseille Universit?, Marseille, France; Institut National de la Sant? et de la Recherche M?dicale U631, Marseille, France; Centre National de la Recherche Scientifique Unit? Mixte de Recherche, Marseille, France. > > > Giusti > Corinne > C > > > Luciani > Marie-Fran?oise > MF > > > Golstein > Pierre > P > > > ENG > > JOURNAL ARTICLE > > > 2010 > 8 > 22 > >
> > Autophagy > 101265188 > 1554-8627 > > > > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > 2010 > 7 > 20 > 6 > 0 > > > aheadofprint > > 12750 > 20639697 > > > > > > > > 20626455 > > 2010 > 7 > 19 > >
> > 1462-2920 > > > 2010 > Jul > 7 > > > Environmental microbiology > > The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa. > > > > > Summary The capacity of a bacterial pathogen to produce a disease in a treated host depends on the former's virulence and resistance to antibiotics. Several scattered pieces of evidence suggest that these two characteristics can be influenced by bacterial metabolism. This potential relationship is particularly important upon infection of a host, a situation that demands bacteria adapt their physiology to their new environment, making use of newly available nutrients. To explore the potential cross-talk between bacterial metabolism, antibiotic resistance and virulence, a Pseudomonas aeruginosa model was used. This species is an important opportunistic pathogen intrinsically resistant to many antibiotics. The role of Crc, a global regulator that controls the metabolism of carbon sources and catabolite repression in Pseudomonas, was analysed to determine its contribution to the intrinsic antibiotic resistance and virulence of P. aeruginosa. Using proteomic analyses, high-throughput metabolic tests and functional assays, the present work shows the virulence and antibiotic resistance of this pathogen to be linked to its physiology, and to be under the control (directly or indirectly) of Crc. A P. aeruginosa strain lacking the Crc regulator showed defects in type III secretion, motility, expression of quorum sensing-regulated virulence factors, and was less virulent in a Dictyostelium discoideum model. In addition, this mutant strain was more susceptible to beta-lactams, aminoglycosides, fosfomycin and rifampin. Crc might therefore be a good target in the search for new antibiotics. > > Departamento de Biotecnolog?a Microbiana, Centro Nacional de Biotecnolog?a, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain. > > > Linares > Juan F > JF > > > Moreno > Renata > R > > > Fajardo > Alicia > A > > > Mart?nez-Solano > Laura > L > > > Escalante > Ricardo > R > > > Rojo > Fernando > F > > > Mart?nez > Jos? L > JL > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 07 > >
> > Environ Microbiol > 100883692 > 1462-2912 > > > > > > 2010 > 7 > 15 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > 2010 > 7 > 16 > 6 > 0 > > > aheadofprint > > EMI2292 > 10.1111/j.1462-2920.2010.02292.x > 20626455 > > > > > > > > 20624437 > > 2010 > 7 > 20 > >
> > 1873-5169 > > > 2010 > Jul > 16 > > > Peptides > > Synthesis and biological activity of peptides equivalent to the IP22 repeat motif found in proteins from Dictyostelium and Mimivirus. > > > > > A novel IP22 repeat motif of unknown function was discovered previously that comprises almost the entire structure of cmbB, a calmodulin-binding protein from Dictyostelium discoideum. An analysis of over 2000 IP22 repeats across 130 different proteins from different species allowed us to define a prototypical IP22 repeat: I/LPxxhxxhxhxxxhxxxhxxxx (where L=leucine, I=isoleucine, h=any hydrophobic amino acid, x=any amino acid). Here we describe the synthesis of three peptide variants of the IP22 motif: IP22-1 (IPNSVTSLKFGDGFNQPLTPGT; 22aa); IP22-2 (LPSTLKTISLSNSTDKKIFKNS; 22aa); and, IP22-3 (IPKSLRSLFLGKGYNQPLEF; 20aa) plus a control peptide from the N-term of cmbB (HNMNPFSPQLDEKKNSHIVEY; 21aa). The structure and purity of synthesized peptides were verified by HPLC and mass spectrometry. The peptides all dose-dependently enhanced random cell motility and cAMP-mediated chemotaxis in Dictyostelium but IP22-3 was most effective peaking in activity around 50muM. Fluorescein isothiocyanate (FITC)-conjugated IP22 peptides did not penetrate cells suggesting these peptides affect cell motility via cell surface interactions. Treatment of cells with FITC-IP22 peptides also led to enhanced cell motility equivalent to the non-conjugated peptides. Treatment of IP22-3-stimulated cells with 50muM LY294002, 20muM quinacrine or both suggests that IP22-3 requires both phosphoinositol 3-kinase and phospholipase A2 signaling to elicit its effects, a mechanism unique from EGFL motility enhancing peptides. The mechanism of action and potential uses of IP22 repeat peptides are discussed. > Copyright ? 2010. Published by Elsevier Inc. > > Department of Cell and Systems Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada, L5L 1C6; Department of Biology, University of Toronto at Mississauga, 3359 Mississauga rd. N., Mississauga, Ontario, Canada, L5L 1C6. > > > Catalano > Andrew > A > > > Luo > Wei > W > > > Wang > Yali > Y > > > O'Day > Danton H > DH > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 16 > >
> > Peptides > 8008690 > 0196-9781 > > > > > > 2010 > 6 > 22 > > > 2010 > 7 > 3 > > > 2010 > 7 > 5 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > 2010 > 7 > 14 > 6 > 0 > > > aheadofprint > > S0196-9781(10)00300-1 > 10.1016/j.peptides.2010.07.005 > 20624437 > > > > > > > > 20617172 > > 2010 > 07 > 09 > >
> > 1553-7404 > > 6 > > 2010 > > > PLoS genetics > PLoS Genet. > > Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum. > > e1001013 > > > Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle. > > Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America. > > > Flowers > Jonathan M > JM > > > Li > Si I > SI > > > Stathos > Angela > A > > > Saxer > Gerda > G > > > Ostrowski > Elizabeth A > EA > > > Queller > David C > DC > > > Strassmann > Joan E > JE > > > Purugganan > Michael D > MD > > > eng > > Journal Article > Research Support, U.S. Gov't, Non-P.H.S. > > > 2010 > 07 > 01 > >
> > United States > PLoS Genet > 101239074 > 1553-7390 > > IM > PMC2895654 > > > > > 2010 > 3 > 15 > > > 2010 > 6 > 1 > > > 2010 > 7 > 1 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > 2010 > 7 > 10 > 6 > 0 > > > epublish > > 10.1371/journal.pgen.1001013 > 20617172 > PMC2895654 > > > > > > > > 20610381 > > 2010 > 7 > 8 > >
> > 1083-351X > > > 2010 > Jul > 7 > > > The Journal of biological chemistry > > Expression of actin Tyr53Ala in Dictyostelium disrupts the cytoskeleton and inhibits intracellular and intercellular chemotactic-signaling. > > > > > We showed previously that phosphorylation of Tyr-53, or its mutation to Ala, inhibits actin polymerization in vitro with formation of aggregates of short filaments, and that expression of Y53A-actin in Dictyostelium blocks differentiation and development at the mound stage (Liu et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13694-13699; Liu et al. (2010) J. Biol. Chem. 285, 9729-9739). We now show that expression of Y53A-actin, which does not affect cell growth, phagocytosis or pinocytosis, inhibits the formation of head-to-tail cell streams during cAMP-induced aggregation, although individual amoebae chemotax normally. We show that expression of Y53A-actin causes a 50% reduction of cell-surface cAMP-receptors, and inhibits cAMP-induced increases in adenylyl cyclase A activity, phosphorylation of ERK2 and actin polymerization. Trafficking of vesicles containing adenylyl cyclase A to the rear of the cell and secretion of the ACA-vesicles are also inhibited. The actin cytoskeleton of cells expressing Y53A-actin is characterized by numerous short filaments, and bundled and aggregated filaments similar to the structures formed by copolymerization of purified Y53A-actin and wild-type actin in vitro. This disorganized actin cytoskeleton may be responsible for the inhibition of intracellular and intercellular cAMP signaling in cells expressing F-Y/A-actin. > > NHLBI, NIH, United States; > > > Shu > Shi > S > > > Liu > Xiong > X > > > Kriebel > Paul W > PW > > > Hong > Myoung-Soon > MS > > > Daniels > Mathew P > MP > > > Parent > Carole A > CA > > > Korn > Edward D > ED > > > ENG > > JOURNAL ARTICLE > > > 2010 > 7 > 7 > >
> > J Biol Chem > 2985121R > 0021-9258 > > > > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > 2010 > 7 > 9 > 6 > 0 > > > aheadofprint > > M110.116277 > 10.1074/jbc.M110.116277 > 20610381 > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Fri Jul 23 23:04:38 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 23 Jul 2010 19:04:38 -0400 Subject: [Bioperl-l] reroot looses branch information Message-ID: Hi, I'm playing with some tree methods from Bio::Tree::TreeFunctionI and I found that Bio::Tree::TreeFunctionI::reroot looses the bootstrap support for the branch leading to the ancestor of the new root. Therefore, when calling reroot, I'm using code like my $ancestor = $newroot->ancestor; my $support = $newroot->bootstrap if (defined $ancestor); $tree->reroot($newroot); $ancestor->bootstrap($support) if (defined $support && defined $ancestor); There seems to be some code in reroot() to prevent that but I don't know why this is happening... Could you please check and fix that? Cheers, Robson From jason.stajich at gmail.com Sat Jul 24 16:41:30 2010 From: jason.stajich at gmail.com (Jason Stajich) Date: Sat, 24 Jul 2010 09:41:30 -0700 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <1125612054.776980.1279892924891.JavaMail.root@zimbra> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> Message-ID: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Hi. You should ask questions to the list. There are many who can answer your question there. In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. -Jason. Sent from my iPod On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > Hi Jason Stajich, > > I am using Bioperl and it is very useful. I have a question about > Bio::DB::GenBank. > This is a simple code. > > -------------------------- > > $db = Bio::DB::GenBank->new(); > @ids = ("LOC441435", "X78121"); > foreach $id (@ids){ > $seqobj = $db->get_Seq_by_id($id); > $seqstr = $seqobj->seq(); > print "$>id\n$seqstr\n"; > } > > -------------------------- > > If there is no entry for an ID, I would like to skip it and to get > next one. But this code stops running when an ID does not exist in > genbank. > How can I solve this problem? > > Thanks. > Hongseok Tae > From cjfields at illinois.edu Sat Jul 24 17:00:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 24 Jul 2010 12:00:24 -0500 Subject: [Bioperl-l] Bio::DB::GenBank question In-Reply-To: <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> References: <1125612054.776980.1279892924891.JavaMail.root@zimbra> <82134C5D-9106-4B6F-BDD9-2AD16E8DE5CC@gmail.com> Message-ID: <9F83881D-6C9C-4996-95DF-D98C140DC3EB@illinois.edu> Any reason not to use a stream here? my $io = $db->get_Stream_by_id(\@ids); while (my $seq = $stream->next_seq) { # do stuff here } chris On Jul 24, 2010, at 11:41 AM, Jason Stajich wrote: > Hi. You should ask questions to the list. There are many who can answer your question there. > > In the older versions you can put the retrieve statement in an eval block. I think newer behavior may be only to issue a warning and keep going. > > You may be able to also set verbose to -1 (-verbose => -1) in the initialization of the db obj and see whether it skips or fails on missing ID. > -Jason. > Sent from my iPod > > On Jul 23, 2010, at 6:48, Hongseok Tae wrote: > >> Hi Jason Stajich, >> >> I am using Bioperl and it is very useful. I have a question about Bio::DB::GenBank. >> This is a simple code. >> >> -------------------------- >> >> $db = Bio::DB::GenBank->new(); >> @ids = ("LOC441435", "X78121"); >> foreach $id (@ids){ >> $seqobj = $db->get_Seq_by_id($id); >> $seqstr = $seqobj->seq(); >> print "$>id\n$seqstr\n"; >> } >> >> -------------------------- >> >> If there is no entry for an ID, I would like to skip it and to get next one. But this code stops running when an ID does not exist in genbank. >> How can I solve this problem? >> >> Thanks. >> Hongseok Tae >> > _______________________________________________ > 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 Jul 25 04:38:25 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jul 2010 00:38:25 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 Message-ID: Hi All, Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- MAJ From david.breimann at gmail.com Sun Jul 25 12:17:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 15:17:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") Message-ID: Hi, I'm using bp_genbank2gff3.pl and seems to work fine, but when I use the -y (split) option it always gives an error on the very last line of the genbank, whch is actually "//": For example, Can't use an undefined value as a symbol reference at /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. What's the problem? Thanks, Dave From dan.bolser at gmail.com Sun Jul 25 13:23:35 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 14:23:35 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? Message-ID: Hi all, The following bug report boils down to this question: How should two sequence objects be compared for identity? Does the object override 'eq' or implement an 'identical' method? I found the following apparent bug in Contig.pm while executing the documented 'SYNOPSIS' code: #!/usr/bin/perl -w use strict; use Bio::Assembly::Contig; my $c = Bio::Assembly::Contig-> new( -id => '1' ); my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' ); my $ls_coord = Bio::SeqFeature::Generic-> new( -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); $c->set_seq_coord( $ls_coord, $ls ); Gives the following WARNINGs: --------------------- WARNING --------------------- MSG: Adding sequence r1, which has already been added --------------------------------------------------- --------------------- WARNING --------------------- MSG: Replacing one sequence [r1] --------------------------------------------------- It seems to be a bug in the documented behaviour of set_seq_coord: "If the sequence was previously added using add_seq, its coordinates are changed/set. Otherwise, add_seq is called and the sequence is added to the contig." The offending line in that function seems to be: if( ... && ($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { ... } $self->add_seq($seq); which compares the *passed* sequence object to the sequence string for the *stored* sequence object of the same name. This comparison is always fails if I understood correctly, therefore set_seq_coord always spews warnings if called after add_seq. Out of curiosity, how come I can't just say: my $ls = Bio::LocatableSeq-> new( -seq => 'ACCG-T', -id => 'r1', -alphabet => 'dna' -start => 3, -end => 8, -strand => 1 ); $c->add_seq( $ls ); I hope the above report can be of some use. Sincerely, Dan. From robfsouza at gmail.com Sun Jul 25 14:42:35 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sun, 25 Jul 2010 10:42:35 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Hi Dan, It is been a long time since I last loooked at this but, if I remember correctly, the point is that Bio:: On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: > The following bug report boils down to this question: > How should two sequence objects be compared for identity? Does the > object override 'eq' or implement an 'identical' method? I think an 'identical' or 'equal' method would be the best alternative since having a full method call would allow passing arguments like '-mode => "complete"' to check all sequence features and annotations if they exist and '-mode => "basic"' to check id() and seq() values. Bio::Assembly::Contig depends mostly on the last one, although only id() is tracked most of the time (because of the internal hashes). > I found the following apparent bug in Contig.pm while executing the > documented 'SYNOPSIS' code: [snip] > It seems to be a bug in the documented behaviour of set_seq_coord: > ? ? ? ?"If the sequence was previously added using add_seq, its > coordinates are changed/set. ?Otherwise, add_seq is called and the > sequence is added to the contig." In fact, it should not print warnings all the time.... > The offending line in that function seems to be: > ?if( ... && > ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { > ? ? ? ? ?... > ?} > ?$self->add_seq($seq); > which compares the *passed* sequence object to the sequence string for > the *stored* sequence object of the same name. This comparison is > always fails if I understood correctly, therefore set_seq_coord always > spews warnings if called after add_seq. Not the sequence string, but the objects themselves, i.e. the string perl uses to represent Bio::LocatableSeq objects... it is a memory based version of identical() :) > Out of curiosity, how come I can't just say: > my $ls = Bio::LocatableSeq-> > ?new( -seq ? ? ?=> 'ACCG-T', > ? ? ? -id ? ? ? => 'r1', > ? ? ? -alphabet => 'dna' > ? ? ? -start ? ?=> 3, > ? ? ? -end ? ? ?=> 8, > ? ? ? -strand ? => 1 > ? ? ); > $c->add_seq( $ls ); Oh, I don't remember but it was either a bad design decision I made 8 years ago to acommodate the Bio::Align::AlignI interface or a problem with Bio::SeqFeature::Collection at that time. Whatever the case, it would be nice to change it... you just need to create a Bio::SeqFeature::Generic when add_seq is called. I just won't have time to do it myself so feel free to act... Best, Robson > I hope the above report can be of some use. > > Sincerely, > Dan. > _______________________________________________ > 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 Sun Jul 25 16:35:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:35:42 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: Cheers for the clarification Robson. How come the 'SYNOPSIS' code does produce warnings about replacing the seq? (the workaround is easy enough, don't add_seq, but still...) Since you said 'feel free to act', I have been faffing around here: http://github.com/dbolser/bioperl-live I'm not really sure if that is so useful, please advise. Thanks again for help, Dan. P.S. How come you are not in irc://irc.freenode.net/#bioperl ;-) On 25 July 2010 15:42, Robson de Souza wrote: > Hi Dan, > > It is been a long time since I last loooked at this but, if I remember > correctly, the point is that Bio:: > > On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >> The following bug report boils down to this question: >> How should two sequence objects be compared for identity? Does the >> object override 'eq' or implement an 'identical' method? > > I think an 'identical' or 'equal' method would be the best alternative > since having a full method call would allow passing arguments like > '-mode => "complete"' to check all sequence features and annotations > if they exist and '-mode => "basic"' to check id() and seq() values. > Bio::Assembly::Contig depends mostly on the last one, although only > id() is tracked most of the time (because of the internal hashes). > >> I found the following apparent bug in Contig.pm while executing the >> documented 'SYNOPSIS' code: > [snip] >> It seems to be a bug in the documented behaviour of set_seq_coord: >> ? ? ? ?"If the sequence was previously added using add_seq, its >> coordinates are changed/set. ?Otherwise, add_seq is called and the >> sequence is added to the contig." > > In fact, it should not print warnings all the time.... > >> The offending line in that function seems to be: >> ?if( ... && >> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >> ? ? ? ? ?... >> ?} >> ?$self->add_seq($seq); >> which compares the *passed* sequence object to the sequence string for >> the *stored* sequence object of the same name. This comparison is >> always fails if I understood correctly, therefore set_seq_coord always >> spews warnings if called after add_seq. > > Not the sequence string, but the objects themselves, i.e. the string > perl uses to represent Bio::LocatableSeq objects... it is a memory > based version of identical() :) > >> Out of curiosity, how come I can't just say: >> my $ls = Bio::LocatableSeq-> >> ?new( -seq ? ? ?=> 'ACCG-T', >> ? ? ? -id ? ? ? => 'r1', >> ? ? ? -alphabet => 'dna' >> ? ? ? -start ? ?=> 3, >> ? ? ? -end ? ? ?=> 8, >> ? ? ? -strand ? => 1 >> ? ? ); >> $c->add_seq( $ls ); > > Oh, I don't remember but it was either a bad design decision I made 8 > years ago to acommodate the Bio::Align::AlignI interface or a problem > with Bio::SeqFeature::Collection at that time. Whatever the case, it > would be nice to change it... you just need to create a > Bio::SeqFeature::Generic when > add_seq is called. I just won't have time to do it myself so feel free to act... > > Best, > Robson > >> I hope the above report can be of some use. >> >> Sincerely, >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From dan.bolser at gmail.com Sun Jul 25 16:40:21 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sun, 25 Jul 2010 17:40:21 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? Message-ID: Which objects implement SeqFeatureI, and how should I find that info? Sorry for the gratuitous noobs. Cheers, Dan. From genehack at genehack.org Sun Jul 25 18:06:55 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:06:55 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? Message-ID: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> (This is in reference to: ; sorry I'm not responding to the original message but I wasn't on the list at that point.) There are really two issues being reported here. First, bp_seqfeature_gff3.PLS throws the following error when used with Bio::SeqFeature::Store::DBI::SQLite: > Can't locate object method "gff3_string" via package "Bio::SeqFeature::Generic" at /Users/jhannah/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS line 58. Second, when called on a database that's been built with '$db->no_blobs(1)', the output doesn't actually include any features. I've got a fix for the first bug in . (I've submitted a pull request for that branch to the 'bioperl' user.) Basically, when looping over the feature objects in bp_seqfeature_gff3.PLS, we introspect each one to find out if it supports the gff3_string() or gff_string() methods, and either call the appropriate one or throw an exception. (I considered just calling gff_string() instead of doing the introspection, since (a) that's the interface documented in SeqFeatureI and (b) SeqFeature::Lite, which is the only thing that currently implements gff3_string() _also_ implements gff_string(), which recalls gff3_string() when appropriate, but in the end decided that this way preserves the original intent of the script as much as possible...) I'm working on something that may be a fix for the second issue as well, but thought I'd throw this first bit out for comments, being as this is the first change I've contributed back to the project. thanks, john. From genehack at genehack.org Sun Jul 25 18:36:07 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:36:07 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> Message-ID: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> On Jul 25, 2010, at 2:06 PM, John Anderson wrote: > Second, when called on a database that's been built with '$db->no_blobs(1)', the output [ snip ] I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. (A pull request for this change has been sent to the 'bioperl' user on Github.) thanks, john. From genehack at genehack.org Sun Jul 25 18:58:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 14:58:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > the -y (split) option it always gives an error on the very last line > of the genbank, whch is actually "//": > > For example, > > Can't use an undefined value as a symbol reference at > /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > > What's the problem? > I filed a bug for you; it's #3124 and can be seen at The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS > index 1216810..6bdae9d 100755 > --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > @@ -654,7 +654,7 @@ for my $file ( @files ) { > } > > ## FIXME for piped output w/ split FA files ... > - close($lumpfa_fh); > + close($lumpfa_fh) if $lumpfa_fh; > if (!$split && $outfa && $lump_fh) { > print $lump_fh "##FASTA\n"; # GFF3 spec > open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > > chrs, john. From cjfields at illinois.edu Sun Jul 25 19:18:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:18:41 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> Message-ID: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> On Jul 25, 2010, at 1:36 PM, John Anderson wrote: > On Jul 25, 2010, at 2:06 PM, John Anderson wrote: >> Second, when called on a database that's been built with '$db->no_blobs(1)', the output > [ snip ] > > I just pushed a second changeset to that I believe fixes this problem. It passes all the tests that are run when Build.PL is configured with the "standard" module list, and it generates much more useful output when run through the scripts in Jay's bug report. > > I did not add any tests for the functionality I added, because I'm not sure where the appropriate place to add them is. Feedback on that would be appreciated -- I think it should be possible to turn the test case Jay appended to the original bug report into a rudimentary test of this change. > > (A pull request for this change has been sent to the 'bioperl' user on Github.) > > thanks, > john. On this one (in Bio::DB::SeqFeature::DBI::mysql): if ( $typeid and $db_seqid and $start and $end and $strand ) { # then we're good... } else { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Changing this to the following should work and is more direct: if ( !defined($typeid) || !defined($db_seqid) || !defined($start) || !defined($end) || !defined($strand) ) { my $sql = qq{ SELECT start,end,tag,strand,seqname FROM feature,feature_location,typelist,locationlist WHERE feature.id=feature_location.id AND feature.typeid=typelist.id AND seqid=locationlist.id AND feature.id = ? }; .... } Might even work shortening to a grep: if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} chris From cjfields at illinois.edu Sun Jul 25 19:20:09 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 14:20:09 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: Message-ID: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Pull request was merged into master branch of bioperl-live. Thanks! Oddly, pull requests aren't coming through via the mail list, I'll look into the issue. chris On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use >> the -y (split) option it always gives an error on the very last line >> of the genbank, whch is actually "//": >> >> For example, >> >> Can't use an undefined value as a symbol reference at >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. >> >> What's the problem? >> > > I filed a bug for you; it's #3124 and can be seen at > > The following patch fixes it for me; it can be found in . I've sent a pull request for this change. > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> index 1216810..6bdae9d 100755 >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS >> @@ -654,7 +654,7 @@ for my $file ( @files ) { >> } >> >> ## FIXME for piped output w/ split FA files ... >> - close($lumpfa_fh); >> + close($lumpfa_fh) if $lumpfa_fh; >> if (!$split && $outfa && $lump_fh) { >> print $lump_fh "##FASTA\n"; # GFF3 spec >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; >> >> > > chrs, > john. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From genehack at genehack.org Sun Jul 25 19:48:22 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 15:48:22 -0400 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: On Jul 25, 2010, at 3:18 PM, Chris Fields wrote: > On this one (in Bio::DB::SeqFeature::DBI::mysql): > > if ( $typeid and $db_seqid and $start and $end and $strand ) { Yeah, sorry, that sort of bugged me too, but once I got into testing stuff I forgot to go back and clean it up... > Might even work shortening to a grep: > > if ( grep {!defined($_)} ($typeid, $db_seqid, $start, $end,$strand) ) {...} Ended up with: # if we weren't called with all the params, pull those out of the database too if ( not ( grep { defined($_) } ( ... ))) { ... } because having the negation buried inside the grep block seemed confusing... I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) j. From david.breimann at gmail.com Sun Jul 25 19:52:53 2010 From: david.breimann at gmail.com (David Breimann) Date: Sun, 25 Jul 2010 22:52:53 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. Thanks! On Sun, Jul 25, 2010 at 10:20 PM, Chris Fields wrote: > Pull request was merged into master branch of bioperl-live. Thanks! > > Oddly, pull requests aren't coming through via the mail list, I'll look > into the issue. > > chris > > On Jul 25, 2010, at 1:58 PM, John Anderson wrote: > > > > > On Jul 25, 2010, at 8:17 AM, David Breimann wrote: > > > >> I'm using bp_genbank2gff3.pl and seems to work fine, but when I use > >> the -y (split) option it always gives an error on the very last line > >> of the genbank, whch is actually "//": > >> > >> For example, > >> > >> Can't use an undefined value as a symbol reference at > >> /usr/local/bin/bp_genbank2gff3.pl line 660, line 41443. > >> > >> What's the problem? > >> > > > > I filed a bug for you; it's #3124 and can be seen at < > http://bugzilla.open-bio.org/show_bug.cgi?id=3124> > > > > The following patch fixes it for me; it can be found in < > http://github.com/genehack/bioperl-live/tree/topic/bug-3124>. I've sent a > pull request for this change. > > > >> diff --git a/scripts/Bio-DB-GFF/genbank2gff3.PLS > b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> index 1216810..6bdae9d 100755 > >> --- a/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> +++ b/scripts/Bio-DB-GFF/genbank2gff3.PLS > >> @@ -654,7 +654,7 @@ for my $file ( @files ) { > >> } > >> > >> ## FIXME for piped output w/ split FA files ... > >> - close($lumpfa_fh); > >> + close($lumpfa_fh) if $lumpfa_fh; > >> if (!$split && $outfa && $lump_fh) { > >> print $lump_fh "##FASTA\n"; # GFF3 spec > >> open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; > >> > >> > > > > chrs, > > john. > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From genehack at genehack.org Sun Jul 25 20:05:33 2010 From: genehack at genehack.org (John Anderson) Date: Sun, 25 Jul 2010 16:05:33 -0400 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <139B16C1-C964-4C9A-AB7F-A6566749B215@genehack.org> On Jul 25, 2010, at 3:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view to use to updated version should I first update my clone of bioperl-live (git pull?) then go through the whole build and install again? Or you could just change the one line in the script yourself; that was the only change. > Second, I have just noticed that bp_genbank2gff3.pl returns an error when given a circular genome with a feature that spans the "end" of the genome (e.g., assume the genome size is 1000np and a feature spans join(900..1000,1..100). Could you send me (not the list, just me) an input file that produces this problem? > Finally, is it possible to tell bp_genbank2gff3.pl to extract the features only (no sequences)? Currently I use the -y flag then delete the fasta file. It looks like the '-n' option should do that, but it currently throws a few more errors of the same general type as you were seeing before -- let me look at those... j. From David.Messina at sbc.su.se Sun Jul 25 20:34:42 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 25 Jul 2010 14:34:42 -0600 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> Message-ID: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> On Jul 25, 2010, at 13:48, John Anderson wrote: > > I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) You've probably seen this, right? http://www.bioperl.org/wiki/Bioperl_Best_Practices Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) Thanks for all your work on this, John! Dave From biopython at maubp.freeserve.co.uk Sun Jul 25 21:10:30 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 25 Jul 2010 22:10:30 +0100 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: On Sun, Jul 25, 2010 at 8:52 PM, David Breimann wrote: > Thank you guys. I'm quite new to all this github stuff, so in order to view > to use to updated version should I first update my clone of bioperl-live > (git pull?) then go through the whole build and install again? > > Second, I have just noticed that bp_genbank2gff3.pl returns an error when > given a circular genome with a feature that spans the "end" of the genome > (e.g., assume the genome size is 1000np and a feature spans > join(900..1000,1..100). The GFF3 spec has recently been updated to cover circular genomes explicitly - this script probably needs updating in light of this. Peter From hlapp at drycafe.net Sun Jul 25 21:26:39 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 25 Jul 2010 17:26:39 -0400 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: Message-ID: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > Hi All, > Our BP poster from the conference is available on SlideShare (search > BioPerl ISMB 2010) and on my wiki homepage. Enjoy- If anyone was wondering about the URL: http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 Mark - were you going to post a news item on this? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Sun Jul 25 23:05:49 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:05:49 -0500 Subject: [Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy? In-Reply-To: <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> References: <61C7B400-B214-4AF2-A766-72CF751E0420@genehack.org> <70F3B7F8-E336-4FDF-AD89-4B747CAD380E@genehack.org> <866A00D5-74C2-4710-8872-184926C8B0D8@illinois.edu> <7319DE74-C177-412D-954F-64C06F8510B5@sbc.su.se> Message-ID: <9F8B93B0-40B4-4D36-AFC8-42AB0F640E80@illinois.edu> On Jul 25, 2010, at 3:34 PM, Dave Messina wrote: > On Jul 25, 2010, at 13:48, John Anderson wrote: >> >> I amended topic/bug-3120 and force-pushed it back to my tree; if you prefer the !defined($_) version just let me know -- still trying to get my head around the preferred house coding style. 8^) > > You've probably seen this, right? > > http://www.bioperl.org/wiki/Bioperl_Best_Practices > > Otherwise, do as you see fit, and someone will speak up if there's any egregiously out of style. :) > > Thanks for all your work on this, John! > > > > Dave Agreed, thanks John. I'll pull this into a local branch and test, then pull in if everything's okay. chris From cjfields at illinois.edu Sun Jul 25 23:09:22 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:22 -0500 Subject: [Bioperl-l] BOSC 2010 BioPerl slides Message-ID: <94B38B72-EC74-49AA-B8E6-7E0E0ABDEBFA@illinois.edu> Just a note that, along with Mark's poster, I gave a smallish update on BioPerl at BOSC 2010: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Feedback welcome! chris From cjfields at illinois.edu Sun Jul 25 23:09:35 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:09:35 -0500 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> Message-ID: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > > On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >> Hi All, >> Our BP poster from the conference is available on SlideShare (search BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > > If anyone was wondering about the URL: > > http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > > Mark - were you going to post a news item on this? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== We could do this along with posting the slides for the BOSC BioPerl talk: http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl chris From cjfields at illinois.edu Sun Jul 25 23:11:06 2010 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jul 2010 18:11:06 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl error on last line ("//") In-Reply-To: References: <7BD88A88-F807-476E-8578-DDA3881DF46E@illinois.edu> Message-ID: <9FB52BF8-532C-4FA2-A590-4ECDA9700E8B@illinois.edu> On Jul 25, 2010, at 4:10 PM, Peter wrote: > On Sun, Jul 25, 2010 at 8:52 PM, David Breimann > wrote: >> Thank you guys. I'm quite new to all this github stuff, so in order to view >> to use to updated version should I first update my clone of bioperl-live >> (git pull?) then go through the whole build and install again? >> >> Second, I have just noticed that bp_genbank2gff3.pl returns an error when >> given a circular genome with a feature that spans the "end" of the genome >> (e.g., assume the genome size is 1000np and a feature spans >> join(900..1000,1..100). > > The GFF3 spec has recently been updated to cover circular > genomes explicitly - this script probably needs updating in light > of this. > > Peter We need to add a few tests for circular genomes with BioPerl; I'm pretty sure these currently do not work as expected. chris From grapevine.256 at gmail.com Mon Jul 26 04:27:16 2010 From: grapevine.256 at gmail.com (Vidya Oruganti) Date: Mon, 26 Jul 2010 12:27:16 +0800 Subject: [Bioperl-l] Restriction Analysis Message-ID: Dear All, I am interested in knowing if there is a way to perform the restriction analysis module on many sequences at once. Currently I am retrieving sequences of contigs one by one from genbank and performing the restriction analysis individually. This is the script I am using: use Bio::Restriction::Analysis; use Bio::DB::GenBank; use Data::Dumper; use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); $seq = $gb->get_Seq_by_gi('405830'); # GI Number my $ra = Bio::Restriction::Analysis->new(-seq=>$seq); print "There are ", scalar $ra->zero_cutters->each_enzyme, " enzymes that do not cut\n"; printf "\n%-10s%s\n", 'Enzyme', 'Number of Cuts'; my $all_cutters = $ra->cutters; map { printf "%-10s%s\n", $_->name, $ra->cuts_by_enzyme($_->name) } $all_cutters->each_enzyme; I would like to know whether it would be possible to get an array of sequences from genbank instead of just one and run the restriction analysis on all the sequences at one go and get several outputs at once. I have been able to retrieve more than one sequence from genbank but I'm not able to run the analysis on more than one sequence. Thank you From adsj at novozymes.com Mon Jul 26 07:09:54 2010 From: adsj at novozymes.com (Adam =?iso-8859-1?Q?Sj=F8gren?=) Date: Mon, 26 Jul 2010 09:09:54 +0200 Subject: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 In-Reply-To: <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> (Chris Fields's message of "Sun, 25 Jul 2010 18:09:35 -0500") References: <5C68610D-81B9-4D82-ACF0-E99DD0FAF59E@drycafe.net> <868CD934-E863-43E2-9A51-9619D1E67EF1@illinois.edu> Message-ID: <87eieqen25.fsf@topper.koldfront.dk> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> Our BP poster from the conference is available on SlideShare (search >>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl Any chance of posting these slides for download somewhere that doesn't require creating an account to do so? Best wishes, Adam, just curious. -- Adam Sj?gren adsj at novozymes.com From avilella at gmail.com Mon Jul 26 09:08:32 2010 From: avilella at gmail.com (Albert Vilella) Date: Mon, 26 Jul 2010 10:08:32 +0100 Subject: [Bioperl-l] Run wrappers for BWA and Samtools In-Reply-To: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> References: <7F56A6EEEB0E4EE291D5340F27DF7D3A@NewLife> Message-ID: Hi Mark, First of all, great work. Can I ask if the aim of combining bwa and samtools would be or could be to replicate "maq.pl easyrun" ? Or what would be an alternative for users wanting to do "maq.pl easyrun" for a combination of long and short reads? Cheers, Albert. On Sat, Nov 28, 2009 at 5:23 PM, Mark A. Jensen wrote: > Hi All, > > Run wrappers for the bwa assembler and the samtools suite > are now available as beta in the bioperl-run/trunk. The bwa > wrapper allows you to run a canned assembly pipeline, or > to execute individual bwa components. The assembly pipeline > can return a Bio::Assembly::Scaffold object via the new > Bio::Assembly::IO::sam module in bioperl-live/trunk > (this requires lstein's Bio::DB::Sam, from CPAN). Details at > > http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_BWA > > and, of course, in the pod. > > Cheers, > MAJ > _______________________________________________ > 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 Jul 26 13:38:01 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:38:01 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 Message-ID: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.com > > _______________________________________________ > 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 Jul 26 13:18:56 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:18:56 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Hi Benard, Forwarding to the list for more help for you. You may want to look at the POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to use this module to create an OrthoMCL wrapper. This might be more technical than you want. Maybe a dev on the list would be interested in creating a wrapper using CommandExts. cheers, MAJ ----- Original Message ----- From: "Benard Kulohoma" To: Sent: Wednesday, July 21, 2010 10:58 AM Subject: Inquiry Hi Mark, I just read your bioperl resource on BWA (and here: http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was most helpful. Do you have any idea of how I could use Bioperl to implement OrthoMCL of several bacterial genomes. I would like to find some membrane proteins. Many thanks, Benard PS: I am sorry for spaming/inquiring!! :) -- 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 roy.chaudhuri at gmail.com Mon Jul 26 13:46:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 26 Jul 2010 14:46:49 +0100 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: <4C4D91C9.4090704@gmail.com> Thanks for this Mark. Just in case anyone can't find it, it's here: http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png Roy. On 26/07/2010 14:38, Mark A. Jensen wrote: > missed the list-- > ----- Original Message ----- > From: "Mark A. Jensen" > To: "Adam "Sj?gren"" > Sent: Monday, July 26, 2010 9:37 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > >> There's a png version of the poster on my wiki page >> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >> wiki thinks it should?). Chris, maybe could upload yours to wiki? >> cheers MAJ >> ----- Original Message ----- >> From: "Adam "Sj?gren"" >> To: >> Sent: Monday, July 26, 2010 3:09 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >> >>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >> >>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >> >>>>> Our BP poster from the conference is available on SlideShare (search >>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >> >>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >> >>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >> >> Any chance of posting these slides for download somewhere that doesn't >> require creating an account to do so? >> >> >> Best wishes, >> >> Adam, just curious. >> >> -- >> Adam Sj?gren >> adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 13:46:38 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 09:46:38 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> Message-ID: http://bioperl.org/wiki/Mark_Jensen, it is... ----- Original Message ----- From: "Mark A. Jensen" To: "BioPerl List" Sent: Monday, July 26, 2010 9:38 AM Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 missed the list-- ----- Original Message ----- From: "Mark A. Jensen" To: "Adam "Sj?gren"" Sent: Monday, July 26, 2010 9:37 AM Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > There's a png version of the poster on my wiki page > (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading > my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the > wiki thinks it should?). Chris, maybe could upload yours to wiki? > cheers MAJ > ----- Original Message ----- > From: "Adam "Sj?gren"" > To: > Sent: Monday, July 26, 2010 3:09 AM > Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 > > > On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: > >> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: > >>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: > >>>> Our BP poster from the conference is available on SlideShare (search >>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- > >>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 > >> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl > > Any chance of posting these slides for download somewhere that doesn't > require creating an account to do so? > > > Best wishes, > > Adam, just curious. > > -- > Adam Sj?gren > adsj at novozymes.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 maj at fortinbras.us Mon Jul 26 14:05:12 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 10:05:12 -0400 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: <4C4D91C9.4090704@gmail.com> References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: http://posters.f1000.com/PosterList?posterID=246 ----- Original Message ----- From: "Roy Chaudhuri" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, July 26, 2010 9:46 AM Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > Thanks for this Mark. Just in case anyone can't find it, it's here: > http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png > > Roy. > > On 26/07/2010 14:38, Mark A. Jensen wrote: >> missed the list-- >> ----- Original Message ----- >> From: "Mark A. Jensen" >> To: "Adam "Sj?gren"" >> Sent: Monday, July 26, 2010 9:37 AM >> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >> >> >>> There's a png version of the poster on my wiki page >>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with >>> uploading >>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>> cheers MAJ >>> ----- Original Message ----- >>> From: "Adam "Sj?gren"" >>> To: >>> Sent: Monday, July 26, 2010 3:09 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>> >>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>> >>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>> >>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>> >>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>> >>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>> >>> Any chance of posting these slides for download somewhere that doesn't >>> require creating an account to do so? >>> >>> >>> Best wishes, >>> >>> Adam, just curious. >>> >>> -- >>> Adam Sj?gren >>> adsj at novozymes.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 amackey at virginia.edu Mon Jul 26 14:51:43 2010 From: amackey at virginia.edu (Aaron Mackey) Date: Mon, 26 Jul 2010 10:51:43 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes sense to "wrap" it. See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt -Aaron On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > Hi Benard, > Forwarding to the list for more help for you. You may want to look at the > POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live > distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to > use this module to create an OrthoMCL wrapper. This might be more technical > than you want. Maybe a dev on the list would be interested in creating a > wrapper using CommandExts. > cheers, MAJ > ----- Original Message ----- From: "Benard Kulohoma" < > B.Kulohoma at liverpool.ac.uk> > To: > Sent: Wednesday, July 21, 2010 10:58 AM > Subject: Inquiry > > > Hi Mark, > > I just read your bioperl resource on BWA (and here: > http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was > most helpful. Do you have any idea of how I could use Bioperl to implement > OrthoMCL of several bacterial genomes. I would like to find some membrane > proteins. > > Many thanks, > > Benard > > PS: I am sorry for spaming/inquiring!! :) > > -- > 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. > > > _______________________________________________ > 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 Jul 26 15:05:05 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 10:05:05 -0500 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: <84B78CA5-5D0E-447C-B507-8FCA18EDA7CB@illinois.edu> Agreed; I'm using it locally. I could see subclassing BLAST (or similar) wrappers specifically for the all-v-all portion of the pipeline (for consistency/flexibility), but I get along w/o that. chris On Jul 26, 2010, at 9:51 AM, Aaron Mackey wrote: > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 maj at fortinbras.us Mon Jul 26 15:07:35 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jul 2010 11:07:35 -0400 Subject: [Bioperl-l] Inquiry on OrthoMCL In-Reply-To: References: Message-ID: Maybe not in the sense of CommandExts, but a BioPerl module that does the "13 steps" might be very useful. (Not saying anyone should do it :) ) ----- Original Message ----- From: "Aaron Mackey" To: "Mark A. Jensen" Cc: "BioPerl List" ; "Benard Kulohoma" Sent: Monday, July 26, 2010 10:51 AM Subject: Re: [Bioperl-l] Inquiry on OrthoMCL > OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes > sense to "wrap" it. > > See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt > > -Aaron > > On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen wrote: > >> Hi Benard, >> Forwarding to the list for more help for you. You may want to look at the >> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live >> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to >> use this module to create an OrthoMCL wrapper. This might be more technical >> than you want. Maybe a dev on the list would be interested in creating a >> wrapper using CommandExts. >> cheers, MAJ >> ----- Original Message ----- From: "Benard Kulohoma" < >> B.Kulohoma at liverpool.ac.uk> >> To: >> Sent: Wednesday, July 21, 2010 10:58 AM >> Subject: Inquiry >> >> >> Hi Mark, >> >> I just read your bioperl resource on BWA (and here: >> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was >> most helpful. Do you have any idea of how I could use Bioperl to implement >> OrthoMCL of several bacterial genomes. I would like to find some membrane >> proteins. >> >> Many thanks, >> >> Benard >> >> PS: I am sorry for spaming/inquiring!! :) >> >> -- >> 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. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 Jul 26 15:35:18 2010 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jul 2010 11:35:18 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, I think there are probably several BioPerl classes that implement Bio::SeqFeatureI, like Bio::SeqFeature::Generic. What are you looking for? Scott On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: > Which objects implement SeqFeatureI, and how should I find that info? > > Sorry for the gratuitous noobs. > > Cheers, > Dan. > _______________________________________________ > 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 Mon Jul 26 16:22:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jul 2010 11:22:54 -0500 Subject: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 In-Reply-To: References: <4D8B4E04661E4C22AEA2633B617FCD94@NewLife> <4C4D91C9.4090704@gmail.com> Message-ID: I've added the PDF version of the BOSC 2010 talk and both the PDF and .ppt versions of the ISMB 2010 BioPerl poster here: http://www.bioperl.org/DIST/presentations/ Just a warning, the PDF of the poster has copyright notices all over it (I'll post a clean one if it's emailed to me!). Mark, did you want to make a blog post about these? chris On Jul 26, 2010, at 9:05 AM, Mark A. Jensen wrote: > Thanks Roy. Also just recieved word that it is also at the Faculty of 1000 poster bank: > http://posters.f1000.com/PosterList?posterID=246 > ----- Original Message ----- From: "Roy Chaudhuri" > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Monday, July 26, 2010 9:46 AM > Subject: Re: [Bioperl-l] Fw: BioPerl at 15 poster from ISMB 2010 > > >> Thanks for this Mark. Just in case anyone can't find it, it's here: >> http://www.bioperl.org/w/images/7/71/BioPerl-ISMB2010.png >> >> Roy. >> >> On 26/07/2010 14:38, Mark A. Jensen wrote: >>> missed the list-- >>> ----- Original Message ----- >>> From: "Mark A. Jensen" >>> To: "Adam "Sj?gren"" >>> Sent: Monday, July 26, 2010 9:37 AM >>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>> >>> >>>> There's a png version of the poster on my wiki page >>>> (http://bioperl.org/w/Majensen, I think). I had some weirdness with uploading >>>> my ppt (maybe the conversion from pptx in Ppt doesn't look exactly like the >>>> wiki thinks it should?). Chris, maybe could upload yours to wiki? >>>> cheers MAJ >>>> ----- Original Message ----- >>>> From: "Adam "Sj?gren"" >>>> To: >>>> Sent: Monday, July 26, 2010 3:09 AM >>>> Subject: Re: [Bioperl-l] BioPerl at 15 poster from ISMB 2010 >>>> >>>> >>>> On Sun, 25 Jul 2010 18:09:35 -0500, Chris wrote: >>>> >>>>> On Jul 25, 2010, at 4:26 PM, Hilmar Lapp wrote: >>>> >>>>>> On Jul 25, 2010, at 12:38 AM, Mark A. Jensen wrote: >>>> >>>>>>> Our BP poster from the conference is available on SlideShare (search >>>>>>> BioPerl ISMB 2010) and on my wiki homepage. Enjoy- >>>> >>>>>> http://www.slideshare.net/majensen1/bioperl-poster-t02-ismb-2010 >>>> >>>>> http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl >>>> >>>> Any chance of posting these slides for download somewhere that doesn't >>>> require creating an account to do so? >>>> >>>> >>>> Best wishes, >>>> >>>> Adam, just curious. >>>> >>>> -- >>>> Adam Sj?gren >>>> adsj at novozymes.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 >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Mon Jul 26 17:54:22 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Mon, 26 Jul 2010 13:54:22 -0400 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: > Thanks again Robson, > > One thing I was going to email the list about is a lack of tests for > ace.pm and phrap.pm ... because of missing libs I'm not running the > sam or the maq tests, so any changes that I'm making to Contig.pm / > Scaffold.pm are not really being tested. > > Do you think anyone on the list (or you) would be able to generate a > few hundred tests to help me start modifying code with confidence? I hope so. I was reading Chris's presentation at BOSC and he mentioned that people are working on the support for the samtools so I believe somebody must have a dataset they could share. > One idea was to actually make Contig.pm implement SeqFeatureI, so that > you could call start and end and seq on the contig (consensus) > directly. > > Here are some notes from IRC... > > 04:00 < dbolser> I think "$contig_object->start" is totally reasonable > 04:01 < dbolser> otherwise its something like > "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" > 04:02 < dbolser> (untested ;-) > 09:01 < genehack> dbolser: i think you've got an argument that there should be; > it's probably going to be a lot easier to do that in > something like Biome (i.e., BioPerl in Moose) Never thought about it... but I can see that could be useful when contigs are part of higher level assemblies, like scaffolds or assembled chromosomes, but you could also achieve this by making Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any reason to prefer the Bio::SeqFeatureI interface? > Any reason not to cc this to the list? Lack of attention. I was so concerned about the answer that I didn't notice I pressed "Reply to" :) Best, Robson > Thanks again. > > All the best, > Dan. > > > > > On 26 July 2010 17:23, Robson de Souza wrote: >> Hi, >> >> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>> Cheers for the clarification Robson. >> >> You are welcome :). Thanks for improving my long abandoned child... :) >> >>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>> seq? (the workaround is easy enough, don't add_seq, but still...) >> >> I don't know. I remember testing it while I develop Contig.pm in >> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >> Did you try ace.pm recently? It uses set_seq_coord and this method >> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >> of previous bug reports on ace.pm regarding unexpected warnings... >> note that set_seq_coord calls remove_seq before adding but prints >> another warning. Compare set_seq_coord to add_seq alone and maybe you >> will figure out what is going on... >> >> Regarding why you can't just add Bio::LocatableSeq objects and have >> add_seq just set the coordinates by itself, I investigated my long >> forgotten code and just realized that the whole problem was that the >> coordinates of a Bio::LocatableSeq object represent the location of >> the object in the original sequence (i.e. unaligned read coordinates) >> instead of its coordinates in the aligned consensus sequence. >> Bio::LocatableSeq issues a warning whenever you try to set the object >> start and end coordinates to the gapped consensus coordinates because >> such coordinates lead to a length shorter than the actual read length: >> >> use Bio::LocatableSeq; >> use Bio::SeqFeature::Collection; >> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >> =>"agggcACT-Gccc", -id=>"uga"); >> my $sfc = Bio::SeqFeature::Collection->new(); >> $sfc->add_features([ $ls ]); >> print $sfc->feature_count,"\t",$ls->length."\n"; >> >> Additionally, Bio::LocatableSeq objects do not support the >> primary_tag() method because they are just Bio::RangeI and not >> Bio::SeqFeatureI objects. These two issues prevented me from using >> Bio::LocatableSeq coordinates to represent gapped consensus >> coordinates but the example code above suggests suppressing >> Bio::LocatableSeq warnings and using the object class >> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >> the need for extra Bio::SeqFeature::Generic objects to store read >> coordinates. >> >>> Since you said 'feel free to act', I have been faffing around here: >>> http://github.com/dbolser/bioperl-live >>> I'm not really sure if that is so useful, please advise. >> >> The comments I made above points to one area where you could have some >> improvements in both memory usage and usability: drop the need for >> additional Bio::SeqFeatureI objects to represent gapped consensus >> coordinates. It would require you to check all Contig.pm methods for >> the use of the "_aligned_coord:$readID" tags (I don't expect to see >> any references to this outside Contig.pm) and change set_seq_coord to >> a method that changes/sets the start and end values of the >> Bio::LocatableSeq objects. >> This might be a bit of work so just go for it if you want and have >> time to experiment. >> >> Another detail: could you please replace references in Contig.pm and >> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >> not exists to the correct Bio::* classes? Somebody changed this to the >> wrong names long ago... >> >>> Thanks again for help, >> >> Well these are my thoughts on the matter. Write again if you decide to >> take this on and are unable to make progress. >> Best, >> Robson >> >>> Dan. >>> >>> >>> P.S. >>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>> >>> >>> On 25 July 2010 15:42, Robson de Souza wrote: >>>> Hi Dan, >>>> >>>> It is been a long time since I last loooked at this but, if I remember >>>> correctly, the point is that Bio:: >>>> >>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>> The following bug report boils down to this question: >>>>> How should two sequence objects be compared for identity? Does the >>>>> object override 'eq' or implement an 'identical' method? >>>> >>>> I think an 'identical' or 'equal' method would be the best alternative >>>> since having a full method call would allow passing arguments like >>>> '-mode => "complete"' to check all sequence features and annotations >>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>> id() is tracked most of the time (because of the internal hashes). >>>> >>>>> I found the following apparent bug in Contig.pm while executing the >>>>> documented 'SYNOPSIS' code: >>>> [snip] >>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>> sequence is added to the contig." >>>> >>>> In fact, it should not print warnings all the time.... >>>> >>>>> The offending line in that function seems to be: >>>>> ?if( ... && >>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>> ? ? ? ? ?... >>>>> ?} >>>>> ?$self->add_seq($seq); >>>>> which compares the *passed* sequence object to the sequence string for >>>>> the *stored* sequence object of the same name. This comparison is >>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>> spews warnings if called after add_seq. >>>> >>>> Not the sequence string, but the objects themselves, i.e. the string >>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>> based version of identical() :) >>>> >>>>> Out of curiosity, how come I can't just say: >>>>> my $ls = Bio::LocatableSeq-> >>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>> ? ? ? -id ? ? ? => 'r1', >>>>> ? ? ? -alphabet => 'dna' >>>>> ? ? ? -start ? ?=> 3, >>>>> ? ? ? -end ? ? ?=> 8, >>>>> ? ? ? -strand ? => 1 >>>>> ? ? ); >>>>> $c->add_seq( $ls ); >>>> >>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>> would be nice to change it... you just need to create a >>>> Bio::SeqFeature::Generic when >>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>> >>>> Best, >>>> Robson >>>> >>>>> I hope the above report can be of some use. >>>>> >>>>> Sincerely, >>>>> Dan. >>>>> _______________________________________________ >>>>> 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 Tue Jul 27 08:53:49 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 09:53:49 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 26 July 2010 16:35, Scott Cain wrote: > Hi Dan, > > I think there are probably several BioPerl classes that implement > Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking > for? A way to find what implements what... something like javadoc for bp. Really I'm looking for a nice 'ontology' of SeqFeatures. I was thinking that Contig.pm should implement Bio::SeqFeatureI. > Scott > > > On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >> Which objects implement SeqFeatureI, and how should I find that info? >> >> Sorry for the gratuitous noobs. >> >> Cheers, >> Dan. >> _______________________________________________ >> 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 dan.bolser at gmail.com Tue Jul 27 09:02:05 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Jul 2010 10:02:05 +0100 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On 26 July 2010 18:54, Robson de Souza wrote: > On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >> Thanks again Robson, >> >> One thing I was going to email the list about is a lack of tests for >> ace.pm and phrap.pm ... because of missing libs I'm not running the >> sam or the maq tests, so any changes that I'm making to Contig.pm / >> Scaffold.pm are not really being tested. >> >> Do you think anyone on the list (or you) would be able to generate a >> few hundred tests to help me start modifying code with confidence? > > I hope so. I was reading Chris's presentation at BOSC and he mentioned > that people are working on the support for the samtools so I believe > somebody must have a dataset they could share. Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because I don't have samtools installed. Also, (quick impression) method coverage is limited (Contig.pm has a lot of methods!). I'll try to write some tests for ace.pm and phrap.pm. >> One idea was to actually make Contig.pm implement SeqFeatureI, so that >> you could call start and end and seq on the contig (consensus) >> directly. >> >> Here are some notes from IRC... >> >> 04:00 < dbolser> I think "$contig_object->start" is totally reasonable >> 04:01 < dbolser> otherwise its something like >> "$contig_object->get_feature_collection->get_feature_by_id("_main_contig_feature:".$contig_object->id)->start" >> 04:02 < dbolser> (untested ;-) >> 09:01 < genehack> dbolser: i think you've got an argument that there should be; >> ? ? ? ? ? ? ? ? ?it's probably going to be a lot easier to do that in >> ? ? ? ? ? ? ? ? ?something like Biome (i.e., BioPerl in Moose) > > Never thought about it... but I can see that could be useful when > contigs are part of higher level assemblies, like scaffolds or > assembled chromosomes, but you could also achieve this by making > Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any > reason to prefer the Bio::SeqFeatureI interface? No. I don't have an overview of how the various objects relate to one another, so any choice is more or less arbitrary. I'll try to write a 'Sequence HOWTO'. Thanks again for help, Dan. >> Any reason not to cc this to the list? > > Lack of attention. I was so concerned about the answer that I didn't > notice I pressed "Reply to" :) > Best, > Robson > >> Thanks again. >> >> All the best, >> Dan. >> >> >> >> >> On 26 July 2010 17:23, Robson de Souza wrote: >>> Hi, >>> >>> On Sun, Jul 25, 2010 at 12:35 PM, Dan Bolser wrote: >>>> Cheers for the clarification Robson. >>> >>> You are welcome :). Thanks for improving my long abandoned child... :) >>> >>>> How come the 'SYNOPSIS' code does produce warnings about replacing the >>>> seq? (the workaround is easy enough, don't add_seq, but still...) >>> >>> I don't know. I remember testing it while I develop Contig.pm in >>> parallel to ace.pm and phrap.pm and not seeing unexpected warnings... >>> Did you try ace.pm recently? It uses set_seq_coord and this method >>> calls add_seq, while phrap.pm uses add_seq directly, but I'm unaware >>> of previous bug reports on ace.pm regarding unexpected warnings... >>> note that set_seq_coord calls remove_seq before adding but prints >>> another warning. Compare set_seq_coord to add_seq alone and maybe you >>> will figure out what is going on... >>> >>> Regarding why you can't just add Bio::LocatableSeq objects and have >>> add_seq just set the coordinates by itself, I investigated my long >>> forgotten code and just realized that the whole problem was that the >>> coordinates of a Bio::LocatableSeq object represent the location of >>> the object in the original sequence (i.e. unaligned read coordinates) >>> instead of its coordinates in the aligned consensus sequence. >>> Bio::LocatableSeq issues a warning whenever you try to set the object >>> start and end coordinates to the gapped consensus coordinates because >>> such coordinates lead to a length shorter than the actual read length: >>> >>> use Bio::LocatableSeq; >>> use Bio::SeqFeature::Collection; >>> ?my $ls = Bio::LocatableSeq->new(-start=> 100500, -end => 100503, -seq >>> =>"agggcACT-Gccc", -id=>"uga"); >>> my $sfc = Bio::SeqFeature::Collection->new(); >>> $sfc->add_features([ $ls ]); >>> print $sfc->feature_count,"\t",$ls->length."\n"; >>> >>> Additionally, Bio::LocatableSeq objects do not support the >>> primary_tag() method because they are just Bio::RangeI and not >>> Bio::SeqFeatureI objects. These two issues prevented me from using >>> Bio::LocatableSeq coordinates to represent gapped consensus >>> coordinates but the example code above suggests suppressing >>> Bio::LocatableSeq warnings and using the object class >>> ($feat->isa(Bio::LocatableSeq"")) instead of a regular expression on >>> the primary tag ("_unaligned_coord:$readID") would be enough to avoid >>> the need for extra Bio::SeqFeature::Generic objects to store read >>> coordinates. >>> >>>> Since you said 'feel free to act', I have been faffing around here: >>>> http://github.com/dbolser/bioperl-live >>>> I'm not really sure if that is so useful, please advise. >>> >>> The comments I made above points to one area where you could have some >>> improvements in both memory usage and usability: drop the need for >>> additional Bio::SeqFeatureI objects to represent gapped consensus >>> coordinates. It would require you to check all Contig.pm methods for >>> the use of the "_aligned_coord:$readID" tags (I don't expect to see >>> any references to this outside Contig.pm) and change set_seq_coord to >>> a method that changes/sets the start and end values of the >>> Bio::LocatableSeq objects. >>> This might be a bit of work so just go for it if you want and have >>> time to experiment. >>> >>> Another detail: could you please replace references in Contig.pm and >>> other Bio::Assembly classes POD to Bio::Assembly::* classes that do >>> not exists to the correct Bio::* classes? Somebody changed this to the >>> wrong names long ago... >>> >>>> Thanks again for help, >>> >>> Well these are my thoughts on the matter. Write again if you decide to >>> take this on and are unable to make progress. >>> Best, >>> Robson >>> >>>> Dan. >>>> >>>> >>>> P.S. >>>> How come you are not in irc://irc.freenode.net/#bioperl ;-) >>>> >>>> >>>> On 25 July 2010 15:42, Robson de Souza wrote: >>>>> Hi Dan, >>>>> >>>>> It is been a long time since I last loooked at this but, if I remember >>>>> correctly, the point is that Bio:: >>>>> >>>>> On Sun, Jul 25, 2010 at 9:23 AM, Dan Bolser wrote: >>>>>> The following bug report boils down to this question: >>>>>> How should two sequence objects be compared for identity? Does the >>>>>> object override 'eq' or implement an 'identical' method? >>>>> >>>>> I think an 'identical' or 'equal' method would be the best alternative >>>>> since having a full method call would allow passing arguments like >>>>> '-mode => "complete"' to check all sequence features and annotations >>>>> if they exist and '-mode => "basic"' to check id() and seq() values. >>>>> Bio::Assembly::Contig depends mostly on the last one, although only >>>>> id() is tracked most of the time (because of the internal hashes). >>>>> >>>>>> I found the following apparent bug in Contig.pm while executing the >>>>>> documented 'SYNOPSIS' code: >>>>> [snip] >>>>>> It seems to be a bug in the documented behaviour of set_seq_coord: >>>>>> ? ? ? ?"If the sequence was previously added using add_seq, its >>>>>> coordinates are changed/set. ?Otherwise, add_seq is called and the >>>>>> sequence is added to the contig." >>>>> >>>>> In fact, it should not print warnings all the time.... >>>>> >>>>>> The offending line in that function seems to be: >>>>>> ?if( ... && >>>>>> ? ? ?($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) { >>>>>> ? ? ? ? ?... >>>>>> ?} >>>>>> ?$self->add_seq($seq); >>>>>> which compares the *passed* sequence object to the sequence string for >>>>>> the *stored* sequence object of the same name. This comparison is >>>>>> always fails if I understood correctly, therefore set_seq_coord always >>>>>> spews warnings if called after add_seq. >>>>> >>>>> Not the sequence string, but the objects themselves, i.e. the string >>>>> perl uses to represent Bio::LocatableSeq objects... it is a memory >>>>> based version of identical() :) >>>>> >>>>>> Out of curiosity, how come I can't just say: >>>>>> my $ls = Bio::LocatableSeq-> >>>>>> ?new( -seq ? ? ?=> 'ACCG-T', >>>>>> ? ? ? -id ? ? ? => 'r1', >>>>>> ? ? ? -alphabet => 'dna' >>>>>> ? ? ? -start ? ?=> 3, >>>>>> ? ? ? -end ? ? ?=> 8, >>>>>> ? ? ? -strand ? => 1 >>>>>> ? ? ); >>>>>> $c->add_seq( $ls ); >>>>> >>>>> Oh, I don't remember but it was either a bad design decision I made 8 >>>>> years ago to acommodate the Bio::Align::AlignI interface or a problem >>>>> with Bio::SeqFeature::Collection at that time. Whatever the case, it >>>>> would be nice to change it... you just need to create a >>>>> Bio::SeqFeature::Generic when >>>>> add_seq is called. I just won't have time to do it myself so feel free to act... >>>>> >>>>> Best, >>>>> Robson >>>>> >>>>>> I hope the above report can be of some use. >>>>>> >>>>>> Sincerely, >>>>>> Dan. >>>>>> _______________________________________________ >>>>>> 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 Jul 27 13:45:25 2010 From: scott at scottcain.net (Scott Cain) Date: Tue, 27 Jul 2010 09:45:25 -0400 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: Hi Dan, You might find the deobfuscator helpful: http://bioperl.org/cgi-bin/deob_interface.cgi Scott On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: > On 26 July 2010 16:35, Scott Cain wrote: >> Hi Dan, >> >> I think there are probably several BioPerl classes that implement >> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >> for? > > A way to find what implements what... something like javadoc for bp. > > Really I'm looking for a nice 'ontology' of SeqFeatures. > > I was thinking that Contig.pm should implement Bio::SeqFeatureI. > > >> Scott >> >> >> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>> Which objects implement SeqFeatureI, and how should I find that info? >>> >>> Sorry for the gratuitous noobs. >>> >>> Cheers, >>> Dan. >>> _______________________________________________ >>> 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 >> > -- ------------------------------------------------------------------------ Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 Ontario Institute for Cancer Research From twaddlac at gmail.com Tue Jul 27 14:10:30 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:10:30 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: Hello, I am curious as to how I am supposed to use SeqIO::fastq to read in a fastq file and then obtain the nucleotide sequence from that. I noticed that SeqIO::fastq returns a Seq::Quality object but I haven't seen a method within that module that returns the nucleotide sequence. Please, let me know if you have any suggestions! Thank you very much!! -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 14:16:27 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:16:27 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: Message-ID: <4C4EEA3B.6020803@gmail.com> Hi Alan, Another case for the deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say $seqqual->seq to get the sequence as a string. Cheers. Roy. On 27/07/2010 15:10, Alan Twaddle wrote: > Hello, > > I am curious as to how I am supposed to use SeqIO::fastq to read > in a fastq file and then obtain the nucleotide sequence from that. I > noticed that SeqIO::fastq returns a Seq::Quality object but I haven't > seen a method within that module that returns the nucleotide sequence. > Please, let me know if you have any suggestions! > > Thank you very much!! > From cjfields at illinois.edu Tue Jul 27 14:34:54 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 09:34:54 -0500 Subject: [Bioperl-l] Bug in Contig.pm? How to compare two sequence objects? In-Reply-To: References: Message-ID: On Jul 27, 2010, at 4:02 AM, Dan Bolser wrote: > On 26 July 2010 18:54, Robson de Souza wrote: >> On Mon, Jul 26, 2010 at 12:37 PM, Dan Bolser wrote: >>> Thanks again Robson, >>> >>> One thing I was going to email the list about is a lack of tests for >>> ace.pm and phrap.pm ... because of missing libs I'm not running the >>> sam or the maq tests, so any changes that I'm making to Contig.pm / >>> Scaffold.pm are not really being tested. >>> >>> Do you think anyone on the list (or you) would be able to generate a >>> few hundred tests to help me start modifying code with confidence? >> >> I hope so. I was reading Chris's presentation at BOSC and he mentioned >> that people are working on the support for the samtools so I believe >> somebody must have a dataset they could share. > > Bio::Assembly::IO::sam.pm is tested, but I don't run the tests because > I don't have samtools installed. Also, (quick impression) method > coverage is limited (Contig.pm has a lot of methods!). > > I'll try to write some tests for ace.pm and phrap.pm. Tests are good! >> Never thought about it... but I can see that could be useful when >> contigs are part of higher level assemblies, like scaffolds or >> assembled chromosomes, but you could also achieve this by making >> Contig.pm a Bio::RangeI or, perhaps better, a Bio::LocatableSeq. Any >> reason to prefer the Bio::SeqFeatureI interface? > > No. I don't have an overview of how the various objects relate to one > another, so any choice is more or less arbitrary. I'll try to write a > 'Sequence HOWTO'. > > > Thanks again for help, > Dan. Dan, The current HOWTOs (Beginner's, Feature/Annotation) should have this information, along with the BioPerl tutorial. chris From twaddlac at gmail.com Tue Jul 27 14:38:09 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:38:09 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EEA3B.6020803@gmail.com> References: <4C4EEA3B.6020803@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: > Hi Alan, > > Another case for the deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi > > A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say > $seqqual->seq to get the sequence as a string. > > Cheers. > Roy. > > On 27/07/2010 15:10, Alan Twaddle wrote: >> >> Hello, >> >> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >> in a fastq file and then obtain the nucleotide sequence from that. I >> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >> seen a method within that module that returns the nucleotide sequence. >> Please, let me know if you have any suggestions! >> >> Thank you very much!! >> > > -- Alan Twaddle, B.S. MUC class of 2010 From roy.chaudhuri at gmail.com Tue Jul 27 14:50:21 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 15:50:21 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> Message-ID: <4C4EF22D.6050705@gmail.com> Hi Alan, It sounds like there's a problem with reading in your Fastq file. Are you using the latest BioPerl version? There have been many bug fixes to Bio::SeqIO::fastq over the last couple of years. If you are using an up-to-date BioPerl, please could you send an example Fastq entry which gives the error messages? Roy. On 27/07/2010 15:37, Alan Twaddle wrote: > Whenever I try to access the sequence I get the following error message: > > > --------------------- WARNING --------------------- > MSG: Seq/Qual descriptions don't match; using sequence description > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Fastq sequence/quality data length mismatch error > > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + > --------------------------------------------------- > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Attempting to set the sequence to > [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] > which does not look healthy > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 > STACK: Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 > STACK: Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 > STACK: Bio::LocatableSeq::new > /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 > STACK: Bio::Seq::Meta::Array::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 > STACK: Bio::Seq::Quality::new > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 > STACK: Bio::Seq::SeqFactory::create > /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 > STACK: Bio::SeqIO::fastq::next_seq > /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 > STACK: fastQParser.pl:12 > > > > On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> Another case for the deobfuscator: >> http://bioperl.org/cgi-bin/deob_interface.cgi >> >> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >> $seqqual->seq to get the sequence as a string. >> >> Cheers. >> Roy. >> >> On 27/07/2010 15:10, Alan Twaddle wrote: >>> >>> Hello, >>> >>> I am curious as to how I am supposed to use SeqIO::fastq to read >>> in a fastq file and then obtain the nucleotide sequence from that. I >>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>> seen a method within that module that returns the nucleotide sequence. >>> Please, let me know if you have any suggestions! >>> >>> Thank you very much!! >>> >> >> > > > From twaddlac at gmail.com Tue Jul 27 14:55:58 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 10:55:58 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4EF22D.6050705@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: I'm not certain that I'm using the latest BioPerl, but I can check. In the mean time, I'll send you the example data! @FQ4HLCS02EO12Q region=2 tag=H +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII @FQ4HLCS02EO12T region=2 tag=B +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: > Hi Alan, > > It sounds like there's a problem with reading in your Fastq file. Are you > using the latest BioPerl version? There have been many bug fixes to > Bio::SeqIO::fastq over the last couple of years. If you are using an > up-to-date BioPerl, please could you send an example Fastq entry which gives > the error messages? > > Roy. > > On 27/07/2010 15:37, Alan Twaddle wrote: >> >> Whenever I try to access the sequence I get the following error message: >> >> >> --------------------- WARNING --------------------- >> MSG: Seq/Qual descriptions don't match; using sequence description >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: Fastq sequence/quality data length mismatch error >> >> --------------------------------------------------- >> >> --------------------- WARNING --------------------- >> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >> --------------------------------------------------- >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Attempting to set the sequence to >> >> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >> which does not look healthy >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >> STACK: Bio::PrimarySeq::seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >> STACK: Bio::PrimarySeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >> STACK: Bio::LocatableSeq::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >> STACK: Bio::Seq::Meta::Array::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >> STACK: Bio::Seq::Quality::new >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >> STACK: Bio::Seq::SeqFactory::create >> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >> STACK: Bio::SeqIO::fastq::next_seq >> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >> STACK: fastQParser.pl:12 >> >> >> >> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >> ?wrote: >>> >>> Hi Alan, >>> >>> Another case for the deobfuscator: >>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>> $seqqual->seq to get the sequence as a string. >>> >>> Cheers. >>> Roy. >>> >>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>> >>>> Hello, >>>> >>>> ? ? ?I am curious as to how I am supposed to use SeqIO::fastq to read >>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>> seen a method within that module that returns the nucleotide sequence. >>>> Please, let me know if you have any suggestions! >>>> >>>> Thank you very much!! >>>> >>> >>> >> >> >> > > -- Alan Twaddle, B.S. MUC class of 2010 From biopython at maubp.freeserve.co.uk Tue Jul 27 15:34:11 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Jul 2010 16:34:11 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > Hopefully this is just an email problem, but that doesn't look like a well formatted FASTQ record to me. Where is the "+" line separating the sequence and qualities? Maybe sending this single record as an attachment would work better (is that encouraged on this mailing list?). Peter From roy.chaudhuri at gmail.com Tue Jul 27 15:35:49 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 16:35:49 +0100 Subject: [Bioperl-l] Fwd: Re: How to Obtain Nucleotide Sequence from SeqIO::fastq Message-ID: <4C4EFCD5.3030809@gmail.com> Forgot to cc the list: -------- Original Message -------- Subject: Re: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq Date: Tue, 27 Jul 2010 16:03:53 +0100 From: Roy Chaudhuri To: Alan Twaddle That doesn't look like Fastq format as defined here: http://nar.oxfordjournals.org/cgi/content/full/gkp1137v1 http://en.wikipedia.org/wiki/FASTQ_format It shouldn't be difficult to write a script to parse it or convert to standard Fastq, though. > p.s. how do I find out what version of bioperl I'm using? http://www.bioperl.org/wiki/FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F On 27/07/2010 15:55, Alan Twaddle wrote: > I'm not certain that I'm using the latest BioPerl, but I can check. In > the mean time, I'll send you the example data! > > @FQ4HLCS02EO12Q region=2 tag=H > +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC > +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII > @FQ4HLCS02EO12T region=2 tag=B > +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC > +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 > > > On Tue, Jul 27, 2010 at 10:50 AM, Roy Chaudhuri wrote: >> Hi Alan, >> >> It sounds like there's a problem with reading in your Fastq file. Are you >> using the latest BioPerl version? There have been many bug fixes to >> Bio::SeqIO::fastq over the last couple of years. If you are using an >> up-to-date BioPerl, please could you send an example Fastq entry which gives >> the error messages? >> >> Roy. >> >> On 27/07/2010 15:37, Alan Twaddle wrote: >>> >>> Whenever I try to access the sequence I get the following error message: >>> >>> >>> --------------------- WARNING --------------------- >>> MSG: Seq/Qual descriptions don't match; using sequence description >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: Fastq sequence/quality data length mismatch error >>> >>> --------------------------------------------------- >>> >>> --------------------- WARNING --------------------- >>> MSG: seq doesn't validate with [0-9A-Za-z\*\-\.=~\\/\?], mismatch is + >>> --------------------------------------------------- >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Attempting to set the sequence to >>> >>> [+GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC] >>> which does not look healthy >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357 >>> STACK: Bio::PrimarySeq::seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:270 >>> STACK: Bio::PrimarySeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/PrimarySeq.pm:221 >>> STACK: Bio::LocatableSeq::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/LocatableSeq.pm:109 >>> STACK: Bio::Seq::Meta::Array::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Meta/Array.pm:167 >>> STACK: Bio::Seq::Quality::new >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/Quality.pm:191 >>> STACK: Bio::Seq::SeqFactory::create >>> /usr/lib/perl5/site_perl/5.8.8/Bio/Seq/SeqFactory.pm:116 >>> STACK: Bio::SeqIO::fastq::next_seq >>> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/fastq.pm:151 >>> STACK: fastQParser.pl:12 >>> >>> >>> >>> On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri >>> wrote: >>>> >>>> Hi Alan, >>>> >>>> Another case for the deobfuscator: >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say >>>> $seqqual->seq to get the sequence as a string. >>>> >>>> Cheers. >>>> Roy. >>>> >>>> On 27/07/2010 15:10, Alan Twaddle wrote: >>>>> >>>>> Hello, >>>>> >>>>> I am curious as to how I am supposed to use SeqIO::fastq to read >>>>> in a fastq file and then obtain the nucleotide sequence from that. I >>>>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't >>>>> seen a method within that module that returns the nucleotide sequence. >>>>> Please, let me know if you have any suggestions! >>>>> >>>>> Thank you very much!! >>>>> >>>> >>>> >>> >>> >>> >> >> > > > From cjfields at illinois.edu Tue Jul 27 15:57:43 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 10:57:43 -0500 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <41845A39-5F63-434A-92E6-86C4CA44C89B@illinois.edu> On Jul 27, 2010, at 10:34 AM, Peter wrote: > On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle wrote: >> I'm not certain that I'm using the latest BioPerl, but I can check. In >> the mean time, I'll send you the example data! >> >> @FQ4HLCS02EO12Q region=2 tag=H >> +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC >> +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII >> @FQ4HLCS02EO12T region=2 tag=B >> +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC >> +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5 >> > > Hopefully this is just an email problem, but that doesn't look like a > well formatted > FASTQ record to me. Where is the "+" line separating the sequence and qualities? > > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). > > Peter As long as the attachment isn't many MB in size, I don't have a problem. Might get delayed by any spam filters though. chris From David.Messina at sbc.su.se Tue Jul 27 16:18:17 2010 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 27 Jul 2010 10:18:17 -0600 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> Message-ID: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> > Maybe sending this single record as an attachment would work better (is that > encouraged on this mailing list?). Absolutely, please try resending as an attachment, Alan. Dave From david.breimann at gmail.com Sat Jul 24 06:47:43 2010 From: david.breimann at gmail.com (David B) Date: Fri, 23 Jul 2010 23:47:43 -0700 (PDT) Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date Message-ID: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Hi, I'm a bit confused about what is the best way to install and maintain the latest updates for bio perl (I'm working on linux). "Installing Bioperl for Unix" (http://www.bioperl.org/wiki/ Installing_Bioperl_for_Unix) suggests using Build.PL or CPAN, but then again I also know that bioperl is currently developed using github (although I know very little about github). 1. Is installing from github an alternative to Build.pL/CPAN options? 2. Does installing from github simply mean cloning than adding the path to PERL5LIB? That's it? 3. I want to use bp_genbank2gff3.pl for circular genomes and I was told I'd better use the developers release of bioperl because only it handles circular genomes correctly. Does it mean I need to clone ...- dev instead of -live and replace the path accordingly? Thanks, David From david.breimann at gmail.com Sat Jul 24 08:06:19 2010 From: david.breimann at gmail.com (David Breimann) Date: Sat, 24 Jul 2010 11:06:19 +0300 Subject: [Bioperl-l] bp_genbank2gff3.pl Message-ID: Hello, I'm trying to convert some genbank files downloaded from NCBI to GFF3 format but I keep getting error messages. My bioperl version (according to perl -MBio::Perl -le 'print Bio::Perl->VERSION;') is 1.0069 (I use github live branch). For example, I am trying to convert CP000249.gbk (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk): $ bp_genbank2gff3.pl CP000249.gbk # Input: CP000249.gbk # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia sp. CcI3, complete genome. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: must be scalar or CODE ref STACK: Error::throw STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/Root.pm:473 STACK: Bio::SeqFeature::Tools::TypeMapper::map_types /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 STACK: /usr/local/bin/bp_genbank2gff3.pl:411 ----------------------------------------------------------- Thanks, David From sc.ncrna at gmail.com Sun Jul 25 13:56:02 2010 From: sc.ncrna at gmail.com (ncRNA) Date: Sun, 25 Jul 2010 06:56:02 -0700 (PDT) Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination Message-ID: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Hi all, I am new to this forum and bioperl. I have a list of mouse genomic regions and would like to get the "corresponding" human genomic sequences, which can be seen from the comparative genomics tracks in the UCSC genome browser. Does anyone have any clue on how to realize this? Thanks in advance, ncRNA From twaddlac at gmail.com Tue Jul 27 16:36:43 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 12:36:43 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: Here's some of the data I would like to parse; the entire file was too big to send via email. Also, if there is some problem with the data, I would appreciate any scripting advice since I am unfortunately a noob :-/ Let me know what you think! Thank you all very much! On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >> Maybe sending this single record as an attachment would work better (is that >> encouraged on this mailing list?). > > Absolutely, please try resending as an attachment, Alan. > > > Dave > > -- Alan Twaddle, B.S. MUC class of 2010 -------------- next part -------------- A non-text attachment was scrubbed... Name: exampleData.fastq Type: application/octet-stream Size: 5510 bytes Desc: not available URL: From cjfields at illinois.edu Tue Jul 27 16:55:26 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 11:55:26 -0500 Subject: [Bioperl-l] How to extract corresponding human genome sequence using mouse genome coordination In-Reply-To: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> References: <3ff3b649-6f10-4f0a-96d1-7e7fb1834d68@d17g2000yqb.googlegroups.com> Message-ID: <2F614027-844E-43EA-8C01-D7C5C7EBF5E5@illinois.edu> Look at the ensembl API for this (I think compara in particular). chris On Jul 25, 2010, at 8:56 AM, ncRNA wrote: > Hi all, > > I am new to this forum and bioperl. I have a list of mouse genomic > regions and would like to get the "corresponding" human genomic > sequences, which can be seen from the comparative genomics tracks in > the UCSC genome browser. Does anyone have any clue on how to realize > this? > > Thanks in advance, > ncRNA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Tue Jul 27 17:14:48 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Tue, 27 Jul 2010 18:14:48 +0100 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> Message-ID: <4C4F1408.3090707@gmail.com> Hi Alan, It looks like there wasn't any problem with the earlier e-mail, and that your file is not Fastq, but rather some unusual Fastq-like format - where did you get the file from? Here's a one-liner to convert your file into standard Fastq: perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < exampleData.fastq > standard.fastq I've assumed that your sequences and qualities are all single-line with a + prefix. Once you have a standard Fastq file you should be able to parse it with BioPerl. Roy. On 27/07/2010 17:36, Alan Twaddle wrote: > Here's some of the data I would like to parse; the entire file was too > big to send via email. Also, if there is some problem with the data, I > would appreciate any scripting advice since I am unfortunately a noob > :-/ > > Let me know what you think! > > Thank you all very much! > > On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina wrote: >>> Maybe sending this single record as an attachment would work better (is that >>> encouraged on this mailing list?). >> >> Absolutely, please try resending as an attachment, Alan. >> >> >> Dave >> >> > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From twaddlac at gmail.com Tue Jul 27 18:57:16 2010 From: twaddlac at gmail.com (Alan Twaddle) Date: Tue, 27 Jul 2010 14:57:16 -0400 Subject: [Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq In-Reply-To: <4C4F1408.3090707@gmail.com> References: <4C4EEA3B.6020803@gmail.com> <4C4EF22D.6050705@gmail.com> <1FAF8854-F145-4D47-83A3-C2B908C0E5A1@sbc.su.se> <4C4F1408.3090707@gmail.com> Message-ID: Ahh thank you very much, everyone!!!! The data was from a GS-FLX Titanium sequencer but it was parsed out of a database into the format that was the "incorrect" fastq style. However, the script worked (though I'm not confident I understand what it just did) and I have successfully parsed the data out of it via BioPerl! Thanks again!! On Tue, Jul 27, 2010 at 1:14 PM, Roy Chaudhuri wrote: > Hi Alan, > > It looks like there wasn't any problem with the earlier e-mail, and that > your file is not Fastq, but rather some unusual Fastq-like format - where > did you get the file from? > > Here's a one-liner to convert your file into standard Fastq: > > perl -ne 'print; $_=<>; s/^\+//; print; $_=<>; s/^\+//; print "+\n$_";' < > exampleData.fastq > standard.fastq > > I've assumed that your sequences and qualities are all single-line with a + > prefix. > > Once you have a standard Fastq file you should be able to parse it with > BioPerl. > > Roy. > > On 27/07/2010 17:36, Alan Twaddle wrote: >> >> Here's some of the data I would like to parse; the entire file was too >> big to send via email. Also, if there is some problem with the data, I >> would appreciate any scripting advice since I am unfortunately a noob >> :-/ >> >> Let me know what you think! >> >> Thank you all very much! >> >> On Tue, Jul 27, 2010 at 12:18 PM, Dave Messina >> ?wrote: >>>> >>>> Maybe sending this single record as an attachment would work better (is >>>> that >>>> encouraged on this mailing list?). >>> >>> Absolutely, please try resending as an attachment, Alan. >>> >>> >>> Dave >>> >>> >> >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Alan Twaddle, B.S. MUC class of 2010 From cjm at berkeleybop.org Tue Jul 27 22:14:00 2010 From: cjm at berkeleybop.org (Chris Mungall) Date: Tue, 27 Jul 2010 15:14:00 -0700 Subject: [Bioperl-l] bp_genbank2gff3.pl In-Reply-To: References: Message-ID: Hi David I can't replicate this, but I just pushed a change that gives more informative error messages on the 'circular' branch (same branch I pushed the unflattener temp fix for circular genomes) On Jul 24, 2010, at 1:06 AM, David Breimann wrote: > Hello, > > I'm trying to convert some genbank files downloaded from NCBI to GFF3 > format but I keep getting error messages. > > My bioperl version (according to perl -MBio::Perl -le 'print > Bio::Perl->VERSION;') is 1.0069 (I use github live branch). > > For example, I am trying to convert CP000249.gbk > (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Frankia_CcI3/CP000249.gbk > ): > > $ bp_genbank2gff3.pl CP000249.gbk > # Input: CP000249.gbk > # working on region:CP000249, Frankia sp. CcI3, 11-MAR-2010, Frankia > sp. CcI3, complete genome. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: must be scalar or CODE ref > STACK: Error::throw > STACK: Bio::Root::Root::throw /home/dave/bioperl-live/Bio/Root/ > Root.pm:473 > STACK: Bio::SeqFeature::Tools::TypeMapper::map_types > /home/dave/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm:195 > STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:930 > STACK: /usr/local/bin/bp_genbank2gff3.pl:411 > ----------------------------------------------------------- > > Thanks, > David > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lairdm at sfu.ca Tue Jul 27 23:55:08 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 16:55:08 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ Message-ID: <4C4F71DC.7090503@sfu.ca> Good day, Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? Unfortunately the + sign in the name makes it a little hard to google. :) Thanks. From cjfields at illinois.edu Wed Jul 28 01:29:52 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jul 2010 20:29:52 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4F71DC.7090503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> Message-ID: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > Good day, > > Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? > > Unfortunately the + sign in the name makes it a little hard to google. :) > > Thanks. Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: http://www.bioperl.org/wiki/HOWTO:BlastPlus chris From maj at fortinbras.us Wed Jul 28 04:51:03 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 28 Jul 2010 00:51:03 -0400 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <9BBF74930A5B477FACC15A4E72E98679@NewLife> >is not backward compatible with StandAloneBlast code, which is a feature, not a >bug ;> If that's not the nicest thing anyone's ever said.... ----- Original Message ----- From: "Chris Fields" To: "Matthew Laird" Cc: Sent: Tuesday, July 27, 2010 9:29 PM Subject: Re: [Bioperl-l] StandAloneBlast & BLAST+ > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the >> docs, and based on my quick testing the answer appears to be no, but does >> Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ > (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and > am trying to get our cluster switched over to it as well. It is not backward > compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get > the github version for this. There is also a bit of online documentation on > this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From lairdm at sfu.ca Wed Jul 28 05:14:05 2010 From: lairdm at sfu.ca (Matthew Laird) Date: Tue, 27 Jul 2010 22:14:05 -0700 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> Message-ID: <4C4FBC9D.2020503@sfu.ca> Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... Thanks for the work guys, we couldn't do it without Bioperl at the core. On 10-07-27 06:29 PM, Chris Fields wrote: > On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: > >> Good day, >> >> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >> >> Unfortunately the + sign in the name makes it a little hard to google. :) >> >> Thanks. > > Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> > > Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: > > http://www.bioperl.org/wiki/HOWTO:BlastPlus > > chris From dan.bolser at gmail.com Wed Jul 28 09:59:39 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 10:59:39 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 27 July 2010 14:45, Scott Cain wrote: > Hi Dan, > > You might find the deobfuscator helpful: > > ?http://bioperl.org/cgi-bin/deob_interface.cgi I've tried to use that, but I don't understand how to get it to list the objects that implement a certain interface. > Scott > > > On Tue, Jul 27, 2010 at 4:53 AM, Dan Bolser wrote: >> On 26 July 2010 16:35, Scott Cain wrote: >>> Hi Dan, >>> >>> I think there are probably several BioPerl classes that implement >>> Bio::SeqFeatureI, like Bio::SeqFeature::Generic. ?What are you looking >>> for? >> >> A way to find what implements what... something like javadoc for bp. >> >> Really I'm looking for a nice 'ontology' of SeqFeatures. >> >> I was thinking that Contig.pm should implement Bio::SeqFeatureI. >> >> >>> Scott >>> >>> >>> On Sun, Jul 25, 2010 at 12:40 PM, Dan Bolser wrote: >>>> Which objects implement SeqFeatureI, and how should I find that info? >>>> >>>> Sorry for the gratuitous noobs. >>>> >>>> Cheers, >>>> Dan. >>>> _______________________________________________ >>>> 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 >>> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net > GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087 > Ontario Institute for Cancer Research > From dan.bolser at gmail.com Wed Jul 28 10:07:38 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jul 2010 11:07:38 +0100 Subject: [Bioperl-l] Newbie question: getting latest version and keeping up to date In-Reply-To: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> References: <1a435321-69ac-4fd2-b753-03cf988c047f@g35g2000yqa.googlegroups.com> Message-ID: On 24 July 2010 07:47, David B wrote: > Hi, > 1. Is installing from github an alternative to Build.pL/CPAN options? Yes, see this page: http://www.bioperl.org/wiki/Using_Git > 2. Does installing from github simply mean cloning than adding the > path to PERL5LIB? That's it? You could do that, or you could apply 'the mantra': perl Build.PL ./Build test ./Build install Don't forget to complain about all failed tests to the appropriate maintainers. > 3. I want to use bp_genbank2gff3.pl for circular genomes and I was > told I'd better use the developers release of bioperl because only it > handles circular genomes correctly. Does it mean I need to clone ...- > dev instead of -live and replace the path accordingly? AFAICT, bioperl-live is "the developers release". Just don't install "bioperl-dead" ... that's really, really bad. > Thanks, > David > > _______________________________________________ > 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 Jul 28 12:56:41 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 07:56:41 -0500 Subject: [Bioperl-l] StandAloneBlast & BLAST+ In-Reply-To: <4C4FBC9D.2020503@sfu.ca> References: <4C4F71DC.7090503@sfu.ca> <118F0166-95AE-4000-A4E8-DDCF81DAD15A@illinois.edu> <4C4FBC9D.2020503@sfu.ca> Message-ID: <397C1B19-0924-4836-B56F-026779E50943@illinois.edu> I'll be working on a 1.6.2 release very soon (had a slight delay due to problems with circular seqs). But BioPerl-Run and others will also be released as well. On Jul 28, 2010, at 12:14 AM, Matthew Laird wrote: > Thanks, good to know. Is there an estimate when it might be stable in the tarball for bioperl-run? > > I can handle grabbing it from git, however the root of my question is making PSORTb work with BLAST+ out of the box, I've already had one request. And not everyone who tries to install our software is as computationally inclined... > > Thanks for the work guys, we couldn't do it without Bioperl at the core. > > On 10-07-27 06:29 PM, Chris Fields wrote: >> On Jul 27, 2010, at 6:55 PM, Matthew Laird wrote: >> >>> Good day, >>> >>> Hopefully a quick (and non-repeated) question. I can't quite tell from the docs, and based on my quick testing the answer appears to be no, but does Bio::Tools::Run::StandAloneBlast support BLAST+? >>> >>> Unfortunately the + sign in the name makes it a little hard to google. :) >>> >>> Thanks. >> >> Mark Jensen wrote up a new set of modules that run BLAST+ (Bio::Tools::Run::StandAloneBlastPlus). I've used it quite a bit locally, and am trying to get our cluster switched over to it as well. It is not backward compatible with StandAloneBlast code, which is a feature, not a bug ;> >> >> Note that it is available in bioperl-run, not bioperl-live. Also best to get the github version for this. There is also a bit of online documentation on this: >> >> http://www.bioperl.org/wiki/HOWTO:BlastPlus >> >> chris From cjfields at illinois.edu Wed Jul 28 13:33:33 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 08:33:33 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > On 27 July 2010 14:45, Scott Cain wrote: >> Hi Dan, >> >> You might find the deobfuscator helpful: >> >> http://bioperl.org/cgi-bin/deob_interface.cgi > > I've tried to use that, but I don't understand how to get it to list > the objects that implement a certain interface. The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. chris From pengyu.ut at gmail.com Wed Jul 28 22:14:33 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 17:14:33 -0500 Subject: [Bioperl-l] Download sequence by genomic location Message-ID: I could download a sequence by location at genome browser. http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 I know that there are ways to get the sequence. But I don't see a way to get the sequence by location. Could anybody let me know if there is such a function in bioperl? http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database -- Regards, Peng From cjfields at illinois.edu Wed Jul 28 22:39:07 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:39:07 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Not for UCSC (IIRC they specifically requested that we not set this functionality up in case their servers were hit too often). I think Galaxy does this, though, and of course you have EntrezGene and the Ensembl API as alternatives. Might be worth re-checking with the UCSC folks to see what their take is on this now... chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 22:47:08 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 17:47:08 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: Forgot completely, but this should be possible via Bio::DAS: http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm I have used it myself via GBrowse. chris On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database > > -- > Regards, > Peng > _______________________________________________ > 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 Jul 28 22:54:44 2010 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 28 Jul 2010 18:54:44 -0400 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: On Wed, Jul 28, 2010 at 6:14 PM, Peng Yu wrote: > I could download a sequence by location at genome browser. > > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 > > I know that there are ways to get the sequence. But I don't see a way > to get the sequence by location. Could anybody let me know if there is > such a function in bioperl? > > http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database Hi, Peng. You could use the DAS API at the UCSC browser: http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=1:1,1000 The DAS spec is here: http://www.biodas.org/documents/spec-1.53.html And the UCSC FAQ entry is here: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 You could also download the chromosome files from UCSC and then use a FASTA indexing module from bioperl to allow quick random access to the files. I know you are also an R user, so you could use the BSgenome package and the appropriate genome to do the same thing. Sean From pengyu.ut at gmail.com Thu Jul 29 03:40:14 2010 From: pengyu.ut at gmail.com (Peng Yu) Date: Wed, 28 Jul 2010 22:40:14 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: I didn't see a document for Bio::Das in my bioperl, $ perldoc Bio::Das No documentation found for "Bio::Das". $ perldoc Bio::Das::SegmentI $ perldoc Bio::Das::FeatureTypeI I thought that maybe my bioperl installation is corrupted. Then I install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I install it by "cpan -f Bio::Das". I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the example. It seems that the there is still something missing. I guess there must be some problem with my bioperl installation. Shall I reinstall it? Is there an easy fix? $ ./main.pl Using password in unencrypted URI against RFC #2396 recommendation at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm line 331. Must have IO::Socket::SSL installed to use https: urls: Can't locate Net/SSLeay.pm in @INC (@INC contains: /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. BEGIN failed--compilation aborted at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm line 18. Compilation failed in require at (eval 41) line 3. at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm line 200 $ cat main.pl #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new(5); # timeout of 5 sec my @response = $das->dsn('http://stein.cshl.org/perl/das', 'http://genome.cse.ucsc.edu/cgi-bin/das', 'http://user:pass at www.wormbase.org/db/das', 'https://euclid.well.ox.ac.uk/cgi-bin/das', ); for my $url (@response) { if ($url->is_success) { my @dsns = $url->results; print "$url:\t\n"; foreach (@dsns) { print "\t",$_->url,"\t",$_->description,"\n"; } } else { print "$url: ",$url->error,"\n"; } } On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: > Forgot completely, but this should be possible via Bio::DAS: > > http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm > > I have used it myself via GBrowse. > > chris > > On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: > >> I could download a sequence by location at genome browser. >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >> >> I know that there are ways to get the sequence. But I don't see a way >> to get the sequence by location. Could anybody let me know if there is >> such a function in bioperl? >> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >> >> -- >> Regards, >> Peng >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- Regards, Peng From cjfields at illinois.edu Thu Jul 29 04:46:56 2010 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jul 2010 23:46:56 -0500 Subject: [Bioperl-l] Download sequence by genomic location In-Reply-To: References: Message-ID: It's not part of BioPerl, but is on CPAN: http://search.cpan.org/dist/Bio-Das/ You don't appear to be following the Bio::Das API. The following worked for me: #!/usr/bin/env perl use strict; use warnings; use Bio::Das; my $das = Bio::Das->new( -source => 'http://genome.cse.ucsc.edu/cgi-bin/das', -dsn => 'hg18', ); my $segment = $das->segment('1:1,100000'); for my $sf ($segment->features) { printf("%s(%s):%d-%d(%d)\n", $sf->display_name, $sf->primary_tag, $sf->start, $sf->end, $sf->strand); } chris On Jul 28, 2010, at 10:40 PM, Peng Yu wrote: > I didn't see a document for Bio::Das in my bioperl, > > $ perldoc Bio::Das > No documentation found for "Bio::Das". > $ perldoc Bio::Das::SegmentI > $ perldoc Bio::Das::FeatureTypeI > > I thought that maybe my bioperl installation is corrupted. Then I > install Bio::Das (cpan Bio::Das), which was unsuccessful. Then I > install it by "cpan -f Bio::Das". > > I also manually installed IO-Socket-SSL-1.33.tar.gz. Then try the > example. It seems that the there is still something missing. I guess > there must be some problem with my bioperl installation. > > Shall I reinstall it? Is there an easy fix? > > $ ./main.pl > Using password in unencrypted URI against RFC #2396 recommendation at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das/HTTP/Fetch.pm > line 331. > Must have IO::Socket::SSL installed to use https: urls: Can't locate > Net/SSLeay.pm in @INC (@INC contains: > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/5.10.1 > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/x86_64-linux > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1 .) at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > BEGIN failed--compilation aborted at > /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/IO/Socket/SSL.pm > line 18. > Compilation failed in require at (eval 41) line 3. > at /home/pengy/utility/linux/opt/perl-5.10.1/lib/site_perl/5.10.1/Bio/Das.pm > line 200 > > $ cat main.pl > #!/usr/bin/env perl > > use strict; > use warnings; > use Bio::Das; > > my $das = Bio::Das->new(5); # timeout of 5 sec > my @response = $das->dsn('http://stein.cshl.org/perl/das', > 'http://genome.cse.ucsc.edu/cgi-bin/das', > 'http://user:pass at www.wormbase.org/db/das', > 'https://euclid.well.ox.ac.uk/cgi-bin/das', > ); > > for my $url (@response) { > if ($url->is_success) { > my @dsns = $url->results; > print "$url:\t\n"; > foreach (@dsns) { > print "\t",$_->url,"\t",$_->description,"\n"; > } > } else { > print "$url: ",$url->error,"\n"; > } > } > > > On Wed, Jul 28, 2010 at 5:47 PM, Chris Fields wrote: >> Forgot completely, but this should be possible via Bio::DAS: >> >> http://search.cpan.org/~lds/Bio-Das-1.06/Das.pm >> >> I have used it myself via GBrowse. >> >> chris >> >> On Jul 28, 2010, at 5:14 PM, Peng Yu wrote: >> >>> I could download a sequence by location at genome browser. >>> >>> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=166347358&o=38129163&g=getDna&i=mixed&c=chr13&l=38129163&r=38153298&db=mm9&hgsid=166347358 >>> >>> I know that there are ways to get the sequence. But I don't see a way >>> to get the sequence by location. Could anybody let me know if there is >>> such a function in bioperl? >>> http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_database >>> >>> -- >>> Regards, >>> Peng >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > > -- > Regards, > Peng > _______________________________________________ > 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 Thu Jul 29 08:08:46 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 09:08:46 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 28 July 2010 14:33, Chris Fields wrote: > On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: > >> On 27 July 2010 14:45, Scott Cain wrote: >>> Hi Dan, >>> >>> You might find the deobfuscator helpful: >>> >>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >> >> I've tried to use that, but I don't understand how to get it to list >> the objects that implement a certain interface. > > The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. OK, so at least I'm not being totally dumb when I can't find this info easily... I'll see if I can script it and add the results to the wiki. > chris From cjfields at illinois.edu Thu Jul 29 13:15:11 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jul 2010 08:15:11 -0500 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > On 28 July 2010 14:33, Chris Fields wrote: >> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >> >>> On 27 July 2010 14:45, Scott Cain wrote: >>>> Hi Dan, >>>> >>>> You might find the deobfuscator helpful: >>>> >>>> http://bioperl.org/cgi-bin/deob_interface.cgi >>> >>> I've tried to use that, but I don't understand how to get it to list >>> the objects that implement a certain interface. >> >> The only way to do this is to introspect every bioperl class. Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. > > OK, so at least I'm not being totally dumb when I can't find this info > easily... I'll see if I can script it and add the results to the wiki. > > >> chris Or, better yet, add it to the /scripts or /examples directory for bioperl-live. Code on the wiki can tend to get lost unless it's in a very accessible place. chris From james-platt at hotmail.co.uk Thu Jul 29 14:18:13 2010 From: james-platt at hotmail.co.uk (James) Date: Thu, 29 Jul 2010 07:18:13 -0700 (PDT) Subject: [Bioperl-l] Newbie question installing on MacOSX Message-ID: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Sorry for the newbie question. I am having trouble installing Bioperl. I'm on MacOSX 10.5.8. I downloaded and installed fink: $ fink --version Package manager version: 0.27.13 Distribution version: 0.9.0 i386 I then downloaded Bioperl-1.6.1, I'm trying to install it from source, as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have Xcode installed etc. '# fink install bioperl-pmXXX' I try this: BioPerl-1.6.1 James$ fink install BioPerl-pm Information about 2521 packages read in 1 seconds. Failed: no package found for specification 'BioPerl-pm'! The version of perl I'm running is 5.8.8, I have tried 'fink install BioPerl588' but this doesn't work either. Thanks very much, James From awitney at sgul.ac.uk Thu Jul 29 15:06:01 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Thu, 29 Jul 2010 16:06:01 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <08188444-D800-43FD-B1BB-4E1B4332BB46@sgul.ac.uk> Hi James, You are mixing up your installation methods. Either install with fink, or download the source and install from there, not both. I would personally recommend installing it from source or better still install from cpan. Take a look here: http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_Build.PL http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN If you really want to use fink then take a look here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink It looks like the command for this is: fink install bioperl-pm588 but I don't use fink any more so I am not certain of how that works. adam On 29 Jul 2010, at 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 15:23:06 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:23:06 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> Message-ID: <4C519CDA.8010008@gmail.com> Hi James, I don't know anything about Macs, but looking here: http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink shouldn't the command be "fink install bioperl-pm588"? Roy. On 29/07/2010 15:18, James wrote: > Sorry for the newbie question. > > I am having trouble installing Bioperl. > > I'm on MacOSX 10.5.8. > > I downloaded and installed fink: > > $ fink --version > Package manager version: 0.27.13 > Distribution version: 0.9.0 i386 > > I then downloaded Bioperl-1.6.1, I'm trying to install it from source, > as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have > Xcode installed etc. > > '# fink install bioperl-pmXXX' > > I try this: > > BioPerl-1.6.1 James$ fink install BioPerl-pm > > Information about 2521 packages read in 1 seconds. > Failed: no package found for specification 'BioPerl-pm'! > > > The version of perl I'm running is 5.8.8, I have tried 'fink install > BioPerl588' but this doesn't work either. > > Thanks very much, > > James > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Thu Jul 29 15:36:11 2010 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Thu, 29 Jul 2010 16:36:11 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> Message-ID: <4C519FEB.8050702@gmail.com> Please copy replies to the mailing list, that way others can respond. Try the command: perl -MBio::Seq -e '' If Bioperl is not installed you will get an error message starting "Can't locate Bio/Seq in @INC". If the command just exits silently then BioPerl is installed correctly. Roy. On 29/07/2010 16:29, James Platt wrote: > Hi, > > I tried that, sorry I wasn't clear in the first post. > > James$ fink install bioperl-pm588 > Information about 2521 packages read in 0 seconds. > Failed: no package found for specification 'bioperl-pm588'! > > I think I may have installed it through fink commander. how do i check > in unix that it is in fact installed? > > Thanks, > > James > > On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: > >> Hi James, >> >> I don't know anything about Macs, but looking here: >> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >> >> shouldn't the command be "fink install bioperl-pm588"? >> >> Roy. >> >> On 29/07/2010 15:18, James wrote: >>> Sorry for the newbie question. >>> >>> I am having trouble installing Bioperl. >>> >>> I'm on MacOSX 10.5.8. >>> >>> I downloaded and installed fink: >>> >>> $ fink --version >>> Package manager version: 0.27.13 >>> Distribution version: 0.9.0 i386 >>> >>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>> source, >>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>> Xcode installed etc. >>> >>> '# fink install bioperl-pmXXX' >>> >>> I try this: >>> >>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>> >>> Information about 2521 packages read in 1 seconds. >>> Failed: no package found for specification 'BioPerl-pm'! >>> >>> >>> The version of perl I'm running is 5.8.8, I have tried 'fink install >>> BioPerl588' but this doesn't work either. >>> >>> Thanks very much, >>> >>> James >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From james-platt at hotmail.co.uk Thu Jul 29 16:11:48 2010 From: james-platt at hotmail.co.uk (James Platt) Date: Thu, 29 Jul 2010 17:11:48 +0100 Subject: [Bioperl-l] Newbie question installing on MacOSX In-Reply-To: <4C519FEB.8050702@gmail.com> References: <6b618068-f0ef-4902-ba96-f731c66c3b72@w30g2000yqw.googlegroups.com> <4C519CDA.8010008@gmail.com> <4C519FEB.8050702@gmail.com> Message-ID: when I'm in the directory it exits silently. When I'm not... James$ perl -MBio::Seq -e '' Can't locate Bio/Seq.pm in @INC (@INC contains: /sw/lib/perl5/darwin- thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/ Updates/5.8.8 /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 .). BEGIN failed--compilation aborted. I guess I need to try install it again. J On 29 Jul 2010, at 16:36, Roy Chaudhuri wrote: > Please copy replies to the mailing list, that way others can respond. > > Try the command: > perl -MBio::Seq -e '' > > If Bioperl is not installed you will get an error message starting > "Can't locate Bio/Seq in @INC". If the command just exits silently > then BioPerl is installed correctly. > > Roy. > > On 29/07/2010 16:29, James Platt wrote: >> Hi, >> >> I tried that, sorry I wasn't clear in the first post. >> >> James$ fink install bioperl-pm588 >> Information about 2521 packages read in 0 seconds. >> Failed: no package found for specification 'bioperl-pm588'! >> >> I think I may have installed it through fink commander. how do i >> check >> in unix that it is in fact installed? >> >> Thanks, >> >> James >> >> On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote: >> >>> Hi James, >>> >>> I don't know anything about Macs, but looking here: >>> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink >>> >>> shouldn't the command be "fink install bioperl-pm588"? >>> >>> Roy. >>> >>> On 29/07/2010 15:18, James wrote: >>>> Sorry for the newbie question. >>>> >>>> I am having trouble installing Bioperl. >>>> >>>> I'm on MacOSX 10.5.8. >>>> >>>> I downloaded and installed fink: >>>> >>>> $ fink --version >>>> Package manager version: 0.27.13 >>>> Distribution version: 0.9.0 i386 >>>> >>>> I then downloaded Bioperl-1.6.1, I'm trying to install it from >>>> source, >>>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have >>>> Xcode installed etc. >>>> >>>> '# fink install bioperl-pmXXX' >>>> >>>> I try this: >>>> >>>> BioPerl-1.6.1 James$ fink install BioPerl-pm >>>> >>>> Information about 2521 packages read in 1 seconds. >>>> Failed: no package found for specification 'BioPerl-pm'! >>>> >>>> >>>> The version of perl I'm running is 5.8.8, I have tried 'fink >>>> install >>>> BioPerl588' but this doesn't work either. >>>> >>>> Thanks very much, >>>> >>>> James >>>> >>>> _______________________________________________ >>>> 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 Thu Jul 29 18:17:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jul 2010 19:17:42 +0100 Subject: [Bioperl-l] What implements SeqFeatureI? In-Reply-To: References: Message-ID: On 29 July 2010 14:15, Chris Fields wrote: > On Jul 29, 2010, at 3:08 AM, Dan Bolser wrote: > >> On 28 July 2010 14:33, Chris Fields wrote: >>> On Jul 28, 2010, at 4:59 AM, Dan Bolser wrote: >>> >>>> On 27 July 2010 14:45, Scott Cain wrote: >>>>> Hi Dan, >>>>> >>>>> You might find the deobfuscator helpful: >>>>> >>>>> ?http://bioperl.org/cgi-bin/deob_interface.cgi >>>> >>>> I've tried to use that, but I don't understand how to get it to list >>>> the objects that implement a certain interface. >>> >>> The only way to do this is to introspect every bioperl class. ?Pprobably recursively parse through all modules looking for package statements, run an eval to load and check the class. >> >> OK, so at least I'm not being totally dumb when I can't find this info >> easily... I'll see if I can script it and add the results to the wiki. >> >> >>> chris > > Or, better yet, add it to the /scripts or /examples directory for bioperl-live. ?Code on the wiki can tend to get lost unless it's in a very accessible place. I meant I'd add the results to the wiki. Nice idea to add the code to the distro. > chris From frederic.romagne at gmail.com Fri Jul 30 04:59:35 2010 From: frederic.romagne at gmail.com (=?ISO-8859-1?Q?Fr=E9d=E9ric_Romagn=E9?=) Date: Fri, 30 Jul 2010 14:59:35 +1000 Subject: [Bioperl-l] phyloxml and element order Message-ID: Hi, I'm using bioperl to create phyloxml trees, after few tentatives, i got my tree with all the element/attributes i want but when I write the tree, element are not written following the order specified in the XSD Schema. For example, i got : Loxosceles intermedia Araneomorphae Sicariidae 969 HAAERADSRKPIWDIAHMVNDLELVD Araneomorphae Sicariidae The program forester complains that should be written before the element. According to http://phyloxml.wordpress.com/2009/11/25/order-of-elements-in-phyloxml this is what bioperl is supposed to do. All my element/attributes are set before writing the tree using 'add_Annotation', 'add_tag_value' and 'sequence' methods from a Bio::Tree::AnnotatableNode object, so i think the error comes from the write_tree method. Any help would be appreciated. Thank you, Fred From com505 at york.ac.uk Fri Jul 30 09:37:11 2010 From: com505 at york.ac.uk (Carrie O'Malley) Date: Fri, 30 Jul 2010 10:37:11 +0100 Subject: [Bioperl-l] installing bioperl Message-ID: Hi there I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. I am not able to complete the installation as every time I get: Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have tried using both methods to install into a local folder and get the same thing !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/home/users/carrieomalley/bin' mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( Many thanks in advance Carrie Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: Data::Stag is not installed (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) CPAN: Storable loaded ok (v2.18) Going to read /Users/carrieomalley/.cpan/Metadata Database was generated on Sat, 10 Jul 2010 11:27:04 GMT Running install for module 'Data::Stag' 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok x Data-Stag-0.11/ x Data-Stag-0.11/c-ext/ x Data-Stag-0.11/c-ext/README.c-ext x Data-Stag-0.11/c-ext/staglib.c x Data-Stag-0.11/c-ext/staglib.h x Data-Stag-0.11/Changes x Data-Stag-0.11/Data/ x Data-Stag-0.11/Data/Stag/ x Data-Stag-0.11/Data/Stag/Arr2HTML.pm x Data-Stag-0.11/Data/Stag/Base.pm x Data-Stag-0.11/Data/Stag/BaseGenerator.pm x Data-Stag-0.11/Data/Stag/BaseHandler.pm x Data-Stag-0.11/Data/Stag/ChainHandler.pm x Data-Stag-0.11/Data/Stag/DTDWriter.pm x Data-Stag-0.11/Data/Stag/GraphHandler.pm x Data-Stag-0.11/Data/Stag/HashDB.pm x Data-Stag-0.11/Data/Stag/IndentParser.pm x Data-Stag-0.11/Data/Stag/IndentWriter.pm x Data-Stag-0.11/Data/Stag/ITextParser.pm x Data-Stag-0.11/Data/Stag/ITextWriter.pm x Data-Stag-0.11/Data/Stag/null.pm x Data-Stag-0.11/Data/Stag/PerlWriter.pm x Data-Stag-0.11/Data/Stag/PodParser.pm x Data-Stag-0.11/Data/Stag/SAX2Stag.pm x Data-Stag-0.11/Data/Stag/Simple.pm x Data-Stag-0.11/Data/Stag/StagDB.pm x Data-Stag-0.11/Data/Stag/StagI.pm x Data-Stag-0.11/Data/Stag/StagImpl.pm x Data-Stag-0.11/Data/Stag/SxprParser.pm x Data-Stag-0.11/Data/Stag/SxprWriter.pm x Data-Stag-0.11/Data/Stag/Util.pm x Data-Stag-0.11/Data/Stag/Writer.pm x Data-Stag-0.11/Data/Stag/XMLParser.pm x Data-Stag-0.11/Data/Stag/XMLWriter.pm x Data-Stag-0.11/Data/Stag/XSLHandler.pm x Data-Stag-0.11/Data/Stag/XSLTHandler.pm x Data-Stag-0.11/Data/Stag.pm x Data-Stag-0.11/dev/ x Data-Stag-0.11/dev/create-manifest.sh x Data-Stag-0.11/dev/data-stag.spec x Data-Stag-0.11/dev/mkspec.pl x Data-Stag-0.11/elisp/ x Data-Stag-0.11/elisp/itext-mode.el x Data-Stag-0.11/homepage/ x Data-Stag-0.11/homepage/archBIG.png x Data-Stag-0.11/homepage/dbstag-tutorial.sgml x Data-Stag-0.11/homepage/images/ x Data-Stag-0.11/homepage/images/k-schema-diagram.png x Data-Stag-0.11/homepage/images/rr-schema-diagram.png x Data-Stag-0.11/homepage/index.html x Data-Stag-0.11/homepage/makefile x Data-Stag-0.11/homepage/mk.sh x Data-Stag-0.11/homepage/mkpodhtml.pl x Data-Stag-0.11/homepage/mkscriptdoc.pl x Data-Stag-0.11/homepage/script-docs/ x Data-Stag-0.11/homepage/script-docs/selectall_html.html x Data-Stag-0.11/homepage/script-docs/selectall_xml.html x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html x Data-Stag-0.11/homepage/script-docs/stag-db.html x Data-Stag-0.11/homepage/script-docs/stag-diff.html x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html x Data-Stag-0.11/homepage/script-docs/stag-elcount.html x Data-Stag-0.11/homepage/script-docs/stag-eval.html x Data-Stag-0.11/homepage/script-docs/stag-filter.html x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html x Data-Stag-0.11/homepage/script-docs/stag-flatten.html x Data-Stag-0.11/homepage/script-docs/stag-grep.html x Data-Stag-0.11/homepage/script-docs/stag-handle.html x Data-Stag-0.11/homepage/script-docs/stag-ir.html x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html x Data-Stag-0.11/homepage/script-docs/stag-join.html x Data-Stag-0.11/homepage/script-docs/stag-merge.html x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html x Data-Stag-0.11/homepage/script-docs/stag-parse.html x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html x Data-Stag-0.11/homepage/script-docs/stag-query.html x Data-Stag-0.11/homepage/script-docs/stag-show-template.html x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html x Data-Stag-0.11/homepage/script-docs/stag-splitter.html x Data-Stag-0.11/homepage/script-docs/stag-storenode.html x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html x Data-Stag-0.11/homepage/script-docs/stag-view.html x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html x Data-Stag-0.11/homepage/script-list.html x Data-Stag-0.11/homepage/stag-db-tutorial.html x Data-Stag-0.11/homepage/stag-poster.html x Data-Stag-0.11/INSTALL x Data-Stag-0.11/Makefile.PL x Data-Stag-0.11/MANIFEST x Data-Stag-0.11/META.yml x Data-Stag-0.11/README x Data-Stag-0.11/scripts/ x Data-Stag-0.11/scripts/stag-autoschema.pl x Data-Stag-0.11/scripts/stag-db.pl x Data-Stag-0.11/scripts/stag-diff.pl x Data-Stag-0.11/scripts/stag-drawtree.pl x Data-Stag-0.11/scripts/stag-elcount.pl x Data-Stag-0.11/scripts/stag-eval.pl x Data-Stag-0.11/scripts/stag-filter.pl x Data-Stag-0.11/scripts/stag-findsubtree.pl x Data-Stag-0.11/scripts/stag-flatten.pl x Data-Stag-0.11/scripts/stag-grep.pl x Data-Stag-0.11/scripts/stag-handle.pl x Data-Stag-0.11/scripts/stag-itext2simple.pl x Data-Stag-0.11/scripts/stag-itext2sxpr.pl x Data-Stag-0.11/scripts/stag-itext2xml.pl x Data-Stag-0.11/scripts/stag-join.pl x Data-Stag-0.11/scripts/stag-merge.pl x Data-Stag-0.11/scripts/stag-mogrify.pl x Data-Stag-0.11/scripts/stag-parse.pl x Data-Stag-0.11/scripts/stag-query.pl x Data-Stag-0.11/scripts/stag-splitter.pl x Data-Stag-0.11/scripts/stag-view.pl x Data-Stag-0.11/scripts/stag-xml2itext.pl x Data-Stag-0.11/scripts/stag-xmlsplit.pl x Data-Stag-0.11/t/ x Data-Stag-0.11/t/animal.x x Data-Stag-0.11/t/autoschema.t x Data-Stag-0.11/t/barfly.x x Data-Stag-0.11/t/bio.x x Data-Stag-0.11/t/chainhandler.t x Data-Stag-0.11/t/collapse.x x Data-Stag-0.11/t/data/ x Data-Stag-0.11/t/data/attrs.xml x Data-Stag-0.11/t/data/bf.txt x Data-Stag-0.11/t/data/eco.el x Data-Stag-0.11/t/data/eco.itext x Data-Stag-0.11/t/data/homol.itext x Data-Stag-0.11/t/data/persons.el x Data-Stag-0.11/t/db.t x Data-Stag-0.11/t/emptytag.t x Data-Stag-0.11/t/get.t x Data-Stag-0.11/t/graph.x x Data-Stag-0.11/t/handlers.t x Data-Stag-0.11/t/handlers2.t x Data-Stag-0.11/t/handlers2.x x Data-Stag-0.11/t/hashdb.t x Data-Stag-0.11/t/hashdb.x x Data-Stag-0.11/t/homol.t x Data-Stag-0.11/t/lisp.x x Data-Stag-0.11/t/parsestr.t x Data-Stag-0.11/t/path.x x Data-Stag-0.11/t/path2.x x Data-Stag-0.11/t/qmatch.t x Data-Stag-0.11/t/roundtrip-attrs.t x Data-Stag-0.11/t/set-attrs.t x Data-Stag-0.11/t/set.t x Data-Stag-0.11/t/sxpr.t x Data-Stag-0.11/t/unhash.t x Data-Stag-0.11/t/unset.t x Data-Stag-0.11/t/write.t x Data-Stag-0.11/t/xml1.t x Data-Stag-0.11/t/xml2.t CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz External Module XML::LibXSLT, XSLT, is not installed on this computer. Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations External Module XML::Parser::PerlSAX, SAX Handler, is not installed on this computer. Data::Stag::XMLParser in Data::Stag needs it for parsing XML External Module GD, Graphical Drawing Toolkit, is not installed on this computer. stag-drawtree.pl in Data::Stag needs it for drawing trees External Module Graph::Directed, Generic Graph data stucture and algorithms, is not installed on this computer. Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs External Module Tk, Tk, is not installed on this computer. stag-view.pl in Data::Stag needs it for tree viewer Information: There are some external packages and perl modules, listed above, which stag uses. This only effects the functionality which is listed above: the rest of stag will work fine, which includes nearly all of the core functionality. Enjoy the rest of stag, which you can use after going 'make install' Checking if your kit is complete... Looks good Writing Makefile for Data Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm cp Data/Stag.pm blib/lib/Data/Stag.pm cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm cp scripts/stag-view.pl blib/script/stag-view.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl cp scripts/stag-grep.pl blib/script/stag-grep.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl cp scripts/stag-merge.pl blib/script/stag-merge.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl cp scripts/stag-parse.pl blib/script/stag-parse.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl cp scripts/stag-join.pl blib/script/stag-join.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl cp scripts/stag-db.pl blib/script/stag-db.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl cp scripts/stag-filter.pl blib/script/stag-filter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl cp scripts/stag-handle.pl blib/script/stag-handle.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl cp scripts/stag-query.pl blib/script/stag-query.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl cp scripts/stag-flatten.pl blib/script/stag-flatten.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl cp scripts/stag-splitter.pl blib/script/stag-splitter.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl cp scripts/stag-diff.pl blib/script/stag-diff.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl Manifying blib/man1/stag-view.pl.1 Manifying blib/man1/stag-mogrify.pl.1 Manifying blib/man1/stag-grep.pl.1 Manifying blib/man1/stag-handle.pl.1 Manifying blib/man1/stag-drawtree.pl.1 Manifying blib/man1/stag-query.pl.1 Manifying blib/man1/stag-merge.pl.1 Manifying blib/man1/stag-parse.pl.1 Manifying blib/man1/stag-findsubtree.pl.1 Manifying blib/man1/stag-join.pl.1 Manifying blib/man1/stag-autoschema.pl.1 Manifying blib/man1/stag-db.pl.1 Manifying blib/man1/stag-flatten.pl.1 Manifying blib/man1/stag-splitter.pl.1 Manifying blib/man1/stag-diff.pl.1 Manifying blib/man1/stag-filter.pl.1 Manifying blib/man3/Data::Stag::StagDB.3pm Manifying blib/man3/Data::Stag::SxprWriter.3pm Manifying blib/man3/Data::Stag.3pm Manifying blib/man3/Data::Stag::ChainHandler.3pm Manifying blib/man3/Data::Stag::IndentParser.3pm Manifying blib/man3/Data::Stag::Simple.3pm Manifying blib/man3/Data::Stag::SAX2Stag.3pm Manifying blib/man3/Data::Stag::Arr2HTML.3pm Manifying blib/man3/Data::Stag::XSLHandler.3pm Manifying blib/man3/Data::Stag::PerlWriter.3pm Manifying blib/man3/Data::Stag::XSLTHandler.3pm Manifying blib/man3/Data::Stag::DTDWriter.3pm Manifying blib/man3/Data::Stag::Writer.3pm Manifying blib/man3/Data::Stag::XMLWriter.3pm Manifying blib/man3/Data::Stag::GraphHandler.3pm Manifying blib/man3/Data::Stag::XMLParser.3pm Manifying blib/man3/Data::Stag::StagImpl.3pm Manifying blib/man3/Data::Stag::PodParser.3pm Manifying blib/man3/Data::Stag::BaseGenerator.3pm Manifying blib/man3/Data::Stag::IndentWriter.3pm Manifying blib/man3/Data::Stag::HashDB.3pm Manifying blib/man3/Data::Stag::null.3pm Manifying blib/man3/Data::Stag::ITextParser.3pm Manifying blib/man3/Data::Stag::BaseHandler.3pm Manifying blib/man3/Data::Stag::ITextWriter.3pm Manifying blib/man3/Data::Stag::SxprParser.3pm CMUNGALL/Data-Stag-0.11.tar.gz make -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/autoschema.........ok t/chainhandler.......ok t/db.................ok t/emptytag...........ok 3/3 skipped: various reasons t/get................ok t/handlers...........ok t/handlers2..........ok 1/9 skipped: various reasons t/hashdb.............ok t/homol..............ok t/parsestr...........ok 6/6 skipped: various reasons t/qmatch.............ok t/roundtrip-attrs....ok 5/5 skipped: various reasons t/set-attrs..........ok 3/3 skipped: various reasons t/set................ok t/sxpr...............ok t/unhash.............ok t/unset..............ok t/write..............ok t/xml1...............ok 7/7 skipped: various reasons t/xml2...............ok 4/4 skipped: various reasons All tests successful, 29 subtests skipped. Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) CMUNGALL/Data-Stag-0.11.tar.gz make test -- OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make install Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1 make: *** [pure_site_install] Error 13 CMUNGALL/Data-Stag-0.11.tar.gz make install -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state *** (back in Bioperl Build.PL) *** Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n - ERROR: You chose to install Data::Stag but it failed to install * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Spreadsheet::ParseExcel is not installed (wanted for parsing Excel files, used by Bio::SeqIO::excel) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite Graph is not installed (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) * Optional prerequisite SVG::Graph is not installed (wanted for creating SVG images, used by Bio::TreeIO::svggraph) * Optional prerequisite SOAP::Lite is not installed (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Convert::Binary::C is not installed (wanted for strider functionality, used by Bio::SeqIO::strider) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite XML::Twig is not installed (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) * Optional prerequisite Set::Scalar is not installed (wanted for proper operation, used by Bio::Tree::Compatible) * Optional prerequisite XML::Parser::PerlSAX is not installed (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite Clone is not installed (wanted for cloning objects, used by Bio::Tools::Primer3) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: BioDBGFF.................disabled * MySQL, Pg nor Oracle DBI drivers are installed BioDBSeqFeature_mysql....disabled - DBD::mysql is not installed Network..................enabled BioDBSeqFeature_BDB......enabled Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] n - will not run internet-requiring tests Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'BioPerl' version '1.006000' Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok 1/28 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 STACK: t/AlignIO/AlignIO.t:51 ----------------------------------------------------------- # Looks like you planned 28 tests but only ran 7. # Looks like your test died just after 7. t/AlignIO/AlignIO............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 8-28 Failed 21/28 tests, 25.00% okay t/AlignIO/arp................................ok 1/48 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. Compilation failed in require at Bio/Root/Root.pm line 420, line 86. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 STACK: t/AlignIO/arp.t:25 ----------------------------------------------------------- # Looks like you planned 48 tests but only ran 2. # Looks like your test died just after 2. t/AlignIO/arp................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-48 Failed 46/48 tests, 4.17% okay 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......................ok 1/159 # Failed test 'use Bio::Annotation::TagTree;' # at t/Annotation/Annotation.t line 20. # Tried to use 'Bio::Annotation::TagTree'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. # Compilation failed in require at (eval 37) line 2. # BEGIN failed--compilation aborted at (eval 37) line 2. t/Annotation/Annotation......................NOK 9/159 # Failed test 'default itext' # at t/Annotation/Annotation.t line 307. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' # Failed test 'itext' # at t/Annotation/Annotation.t line 315. # 'ARRAY(0x100c02a48)' # doesn't match '(?-xism:Name: CALM1)' Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. # Looks like you planned 159 tests but only ran 119. # Looks like you failed 3 tests of 119 run. # Looks like your test died just after 119. t/Annotation/Annotation......................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 9, 117, 119-159 Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................ok 1/51 # Failed (TODO) test at t/Assembly/Assembly.t line 35. t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok 1/24 skipped: various reasons t/Biblio/References..........................ok t/Biblio/biofetch............................skipped all skipped: Network tests have not been requested t/Biblio/eutils..............................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/ClusterIO/ClusterIO........................ok 8/12 skipped: various reasons t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/ClusterIO/SequenceFamily.t:16 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. # Looks like you planned 19 tests but only ran 2. # Looks like your test died just after 2. t/ClusterIO/SequenceFamily...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 3-19 Failed 17/19 tests, 10.53% okay 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 11/279 skipped: various reasons t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 STACK: t/LocalDB/Flat.t:89 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. # Looks like you planned 24 tests but only ran 14. # Looks like your test died just after 14. t/LocalDB/Flat...............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 15-24 Failed 10/24 tests, 58.33% okay t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 STACK: t/LocalDB/Index.t:91 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. # Looks like you planned 64 tests but only ran 31. # Looks like your test died just after 31. t/LocalDB/Index..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 32-64 Failed 33/64 tests, 48.44% okay t/LocalDB/Registry...........................ok 9/14 skipped: various reasons t/LocalDB/SeqFeature.........................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok 19/267 skipped: various reasons 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 10/14 skipped: various reasons t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped all skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok 10/29 skipped: various reasons 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..................................ok t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok 4/46 skipped: various reasons t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................skipped all skipped: Network tests have not been requested t/RemoteDB/CUTG..............................ok 14/37 skipped: various reasons t/RemoteDB/DB................................skipped all skipped: Network tests have not been requested t/RemoteDB/EMBL..............................skipped all skipped: Network tests have not been requested t/RemoteDB/EUtilities........................skipped all skipped: Network tests have not been requested t/RemoteDB/HIV/HIV...........................ok 13/30 skipped: various reasons t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok 10/41 skipped: various reasons t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok 10/16 skipped: various reasons t/RemoteDB/SeqHound..........................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqRead_fail......................skipped all skipped: Network tests have not been requested t/RemoteDB/SeqVersion........................ok 8/10 skipped: various reasons t/RemoteDB/Taxonomy..........................skipped all skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................ok 1/18 # Failed (TODO) test at t/Restriction/IO.t line 31. t/Restriction/IO.............................ok 3/18 skipped: various reasons t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................ok 2/31 skipped: various reasons t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped all 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.............................ok 1/1093 # Failed (TODO) test at t/SearchIO/blast.t line 527. # '0.852' # > # '0.9' # Failed (TODO) test at t/SearchIO/blast.t line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................ok 1/289 # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................ok 1/298 # Failed (TODO) test at t/SearchIO/blastxml.t line 258. # got: undef # expected: '31984247' # Failed (TODO) test at t/SearchIO/blastxml.t line 259. # got: undef # expected: '88780' # Failed (TODO) test at t/SearchIO/blastxml.t line 260. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok 4/45 skipped: various reasons 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...........................ok 1/116 # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. # got: 'Bio::Location::Simple=HASH(0x100838ce8)' # expected: undef # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test at t/Seq/LocatableSeq.t 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 all 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 all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok 7/214 skipped: various reasons t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqIO/Handler.t:20 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. # Looks like you planned 550 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/Handler..............................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 2-550 Failed 549/550 tests, 0.18% okay t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped all 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..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped all skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ # Failed test 'use Bio::SeqIO::chaos;' # at t/SeqIO/chaos.t line 15. # Tried to use 'Bio::SeqIO::chaos'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. # Looks like you failed 1 test of 8. t/SeqIO/chaos................................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/8 tests, 87.50% okay t/SeqIO/chaosxml.............................skipped all skipped: The optional module Data::Stag (or dependencies thereof) was not installed t/SeqIO/ctf..................................skipped all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped all 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 all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................ok 1/17 # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 54. # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped all 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 all 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 all 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..................................ok 1/59 # Failed (TODO) test 'accuracies' # at t/SeqIO/scf.t line 78. # got: 'ARRAY(0x100ac5648)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ # Failed test 'use Bio::SeqIO::swiss;' # at t/SeqIO/swiss.t line 12. # Tried to use 'Bio::SeqIO::swiss'. # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. # Compilation failed in require at (eval 14) line 2. # BEGIN failed--compilation aborted at (eval 14) line 2. Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. # Looks like you planned 240 tests but only ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test died just after 1. t/SeqIO/swiss................................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-240 Failed 240/240 tests, 0.00% okay t/SeqIO/tab..................................ok t/SeqIO/table................................ok 112/450 skipped: various reasons t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped all 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 1/49Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/SeqTools/GuessSeqFormat.t:62 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time t/SeqTools/GuessSeqFormat....................NOK 25/49 # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. # ' # at t/SeqTools/GuessSeqFormat.t line 71. # got: '0' # expected: '1' # Looks like you planned 49 tests but ran 1 extra. # Looks like you failed 1 test of 50 run. t/SeqTools/GuessSeqFormat....................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED tests 25, 50 Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok 5/21 skipped: various reasons t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped all 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 all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut..............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN.................skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos.............skipped all skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. Compilation failed in require at Bio/SeqIO/swiss.pm line 197. BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. Compilation failed in require at Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 STACK: t/Tools/Analysis/Protein/Scansite.t:23 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. # Looks like you planned 14 tests but only ran 4. # Looks like your test died just after 4. t/Tools/Analysis/Protein/Scansite............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 5-14 Failed 10/14 tests, 28.57% okay t/Tools/Analysis/Protein/Sopma...............ok 12/16 skipped: various reasons 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 all 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......................skipped all skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast..................ok 12/45 skipped: various reasons 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 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 all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok 2/74 skipped: various reasons t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................ok t/Tree/TreeIO/svggraph.......................ok 3/4 skipped: various reasons 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 15/26 skipped: various reasons Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/AlignIO/AlignIO.t 255 65280 28 42 8-28 t/AlignIO/arp.t 255 65280 48 92 3-48 t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 t/LocalDB/Flat.t 255 65280 24 20 15-24 t/LocalDB/Index.t 255 65280 64 66 32-64 t/SeqIO/Handler.t 255 65280 550 1098 2-550 t/SeqIO/chaos.t 1 256 8 1 1 t/SeqIO/swiss.t 255 65280 240 479 1-240 t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 57 tests and 313 subtests skipped. Failed 11/318 test scripts. 970/17228 subtests failed. Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) Failed 11/318 test programs. 970/17228 subtests failed. Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 From robfsouza at gmail.com Fri Jul 30 13:54:08 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Fri, 30 Jul 2010 09:54:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Did you try, as root, ./Build.pl --install_base /opt/local ? Also, check the INSTALL file at the root of the bioperl distribution. Robson On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > ?I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > ?- ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > ?is not installed on this computer. > ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > ?is not installed on this computer. > ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > ?is not installed on this computer. > ?stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > ?is not installed on this computer. > ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > ?is not installed on this computer. > ?stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > ? There are some external packages and perl modules, listed above, which > ? stag uses. This only effects the functionality which is listed above: > ? the rest of stag will work fine, which includes nearly all of the > ? core functionality. > > ? Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > ? ? ? ?3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > ? ? ? ?1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > ? ? ? ?6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > ? ? ? ?5/5 skipped: various reasons > t/set-attrs..........ok > ? ? ? ?3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > ? ? ? ?7/7 skipped: various reasons > t/xml2...............ok > ? ? ? ?4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at -e line 1 > make: *** [pure_site_install] Error 13 > ?CMUNGALL/Data-Stag-0.11.tar.gz > ?make install ?-- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > ?- ERROR: You chose to install Data::Stag but it failed to install > ?* Optional prerequisite Ace is not installed > ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > ?* Optional prerequisite Spreadsheet::ParseExcel is not installed > ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) > ?* Optional prerequisite Math::Random is not installed > ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > ?* Optional prerequisite Graph is not installed > ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > ?* Optional prerequisite SVG::Graph is not installed > ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > ?* Optional prerequisite SOAP::Lite is not installed > ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed > ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > ?* Optional prerequisite GraphViz is not installed > ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > ?* Optional prerequisite Array::Compare is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite Convert::Binary::C is not installed > ? (wanted for strider functionality, used by Bio::SeqIO::strider) > ?* Optional prerequisite Algorithm::Munkres is not installed > ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > ?* Optional prerequisite XML::Twig is not installed > ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > ?* Optional prerequisite Set::Scalar is not installed > ? (wanted for proper operation, used by Bio::Tree::Compatible) > ?* Optional prerequisite XML::Parser::PerlSAX is not installed > ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > ?* Optional prerequisite XML::SAX::Writer is not installed > ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) > ?* Optional prerequisite Clone is not installed > ? (wanted for cloning objects, used by Bio::Tools::Primer3) > ?* Optional prerequisite XML::DOM::XPath is not installed > ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > ?* Optional prerequisite PostScript::TextBlock is not installed > ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > ?BioDBGFF.................disabled > ? ?* MySQL, Pg nor Oracle DBI drivers are installed > ?BioDBSeqFeature_mysql....disabled > ? ?- DBD::mysql is not installed > ?Network..................enabled > ?BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > ?- will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > ?- will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > ? ? ? ?Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > ? ? ? ?Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # ? Failed test 'use Bio::Annotation::TagTree;' > # ? at t/Annotation/Annotation.t line 20. > # ? ? Tried to use 'Bio::Annotation::TagTree'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # ? Failed test 'default itext' > # ? at t/Annotation/Annotation.t line 307. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > > # ? Failed test 'itext' > # ? at t/Annotation/Annotation.t line 315. > # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' > # ? ? doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > ? ? ? ?1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > ? ? ? ?8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > ? ? ? ?Failed 17/19 tests, 10.53% okay > 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 > ? ? ? ?11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > ? ? ? ?Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > ? ? ? ?Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > ? ? ? ?9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > ? ? ? ?19/267 skipped: various reasons > 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 > ? ? ? ?10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > ? ? ? ?10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > ? ? ? ?4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > ? ? ? ?14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > ? ? ? ?13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > ? ? ? ?10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > ? ? ? ?10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > ? ? ? ?8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # ? Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > ? ? ? ?3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > ? ? ? ?2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > ? ? ? ?all 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.............................ok 1/1093 > # ? Failed (TODO) test at t/SearchIO/blast.t line 527. > # ? ? '0.852' > # ? ? ? ? > > # ? ? '0.9' > > # ? Failed (TODO) test at t/SearchIO/blast.t line 528. > # ? ? '1.599' > # ? ? ? ? <= > # ? ? '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # ? ? ? ? ?got: '0.946' > # ? ? expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # ? ? ? ? ?got: undef > # ? ? expected: '31984247' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # ? ? ? ? ?got: undef > # ? ? expected: '88780' > > # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # ? ? ? ? ?got: undef > # ? ? expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > ? ? ? ?4/45 skipped: various reasons > 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...........................ok 1/116 > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # ? ? expected: undef > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # ? ? ? ? ?got: '\-\.=~' > # ? ? expected: '-\?' > > # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > ? ? ? ?7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > ? ? ? ?Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > ? ? ? ?all 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..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # ? Failed test 'use Bio::SeqIO::chaos;' > # ? at t/SeqIO/chaos.t line 15. > # ? ? Tried to use 'Bio::SeqIO::chaos'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > ? ? ? ?Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # ? Failed (TODO) test 'primary_id' > # ? at t/SeqIO/gcg.t line 54. > # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # ? ? expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > ? ? ? ?all 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 > ? ? ? ?all 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 > ? ? ? ?all 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..................................ok 1/59 > # ? Failed (TODO) test 'accuracies' > # ? at t/SeqIO/scf.t line 78. > # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' > # ? ? expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # ? Failed test 'use Bio::SeqIO::swiss;' > # ? at t/SeqIO/swiss.t line 12. > # ? ? Tried to use 'Bio::SeqIO::swiss'. > # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > ? ? ? ?Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > ? ? ? ?112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # ? at t/SeqTools/GuessSeqFormat.t line 71. > # ? ? ? ? ?got: '0' > # ? ? expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > ? ? ? ?Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > ? ? ? ?5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > ? ? ? ?all 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 > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > ? ? ? ?Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > ? ? ? ?12/16 skipped: various reasons > 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 > ? ? ? ?all 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......................skipped > ? ? ? ?all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > ? ? ? ?12/45 skipped: various reasons > 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 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 > ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > ? ? ? ?2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > ? ? ? ?3/4 skipped: various reasons > 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 > ? ? ? ?15/26 skipped: various reasons > Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 > t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 > t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 > t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 > t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 > t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 > t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 > t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 > t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 > t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 > t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > 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 Fri Jul 30 15:26:12 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Fri, 30 Jul 2010 16:26:12 +0100 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: <70A35EB0-D004-4B7A-A239-D9EA7F9EA206@sgul.ac.uk> It looks like it is trying to install and failing because of lack of permissions. I would recommend you try the cpan route like this: perl -MCPAN -e shell then from the cpan prompt, set a few things up (only need to do this once): cpan> o conf make_install_make_command 'sudo make' cpan> o conf mbuild_install_build_command 'sudo ./Build' cpan> o conf commit cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz .... and keep an eye on it... it will ask for a password early on to allow it to install into the right directories. Or you if you want to retry your current method you could do this sudo perl ./Build.pl HTH adam On 30 Jul 2010, at 10:37, Carrie O'Malley wrote: > Hi there > I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. > I am not able to complete the installation as every time I get: > > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > I have tried using both methods to install into a local folder and get the same thing > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/home/users/carrieomalley/bin' > mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. > > > If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( > > > Many thanks in advance > Carrie > > > > > > Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL > Checking whether your kit is complete... > Looks good > > Checking prerequisites... > - ERROR: Data::Stag is not installed > (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) > CPAN: Storable loaded ok (v2.18) > Going to read /Users/carrieomalley/.cpan/Metadata > Database was generated on Sat, 10 Jul 2010 11:27:04 GMT > Running install for module 'Data::Stag' > 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' > Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok > x Data-Stag-0.11/ > x Data-Stag-0.11/c-ext/ > x Data-Stag-0.11/c-ext/README.c-ext > x Data-Stag-0.11/c-ext/staglib.c > x Data-Stag-0.11/c-ext/staglib.h > x Data-Stag-0.11/Changes > x Data-Stag-0.11/Data/ > x Data-Stag-0.11/Data/Stag/ > x Data-Stag-0.11/Data/Stag/Arr2HTML.pm > x Data-Stag-0.11/Data/Stag/Base.pm > x Data-Stag-0.11/Data/Stag/BaseGenerator.pm > x Data-Stag-0.11/Data/Stag/BaseHandler.pm > x Data-Stag-0.11/Data/Stag/ChainHandler.pm > x Data-Stag-0.11/Data/Stag/DTDWriter.pm > x Data-Stag-0.11/Data/Stag/GraphHandler.pm > x Data-Stag-0.11/Data/Stag/HashDB.pm > x Data-Stag-0.11/Data/Stag/IndentParser.pm > x Data-Stag-0.11/Data/Stag/IndentWriter.pm > x Data-Stag-0.11/Data/Stag/ITextParser.pm > x Data-Stag-0.11/Data/Stag/ITextWriter.pm > x Data-Stag-0.11/Data/Stag/null.pm > x Data-Stag-0.11/Data/Stag/PerlWriter.pm > x Data-Stag-0.11/Data/Stag/PodParser.pm > x Data-Stag-0.11/Data/Stag/SAX2Stag.pm > x Data-Stag-0.11/Data/Stag/Simple.pm > x Data-Stag-0.11/Data/Stag/StagDB.pm > x Data-Stag-0.11/Data/Stag/StagI.pm > x Data-Stag-0.11/Data/Stag/StagImpl.pm > x Data-Stag-0.11/Data/Stag/SxprParser.pm > x Data-Stag-0.11/Data/Stag/SxprWriter.pm > x Data-Stag-0.11/Data/Stag/Util.pm > x Data-Stag-0.11/Data/Stag/Writer.pm > x Data-Stag-0.11/Data/Stag/XMLParser.pm > x Data-Stag-0.11/Data/Stag/XMLWriter.pm > x Data-Stag-0.11/Data/Stag/XSLHandler.pm > x Data-Stag-0.11/Data/Stag/XSLTHandler.pm > x Data-Stag-0.11/Data/Stag.pm > x Data-Stag-0.11/dev/ > x Data-Stag-0.11/dev/create-manifest.sh > x Data-Stag-0.11/dev/data-stag.spec > x Data-Stag-0.11/dev/mkspec.pl > x Data-Stag-0.11/elisp/ > x Data-Stag-0.11/elisp/itext-mode.el > x Data-Stag-0.11/homepage/ > x Data-Stag-0.11/homepage/archBIG.png > x Data-Stag-0.11/homepage/dbstag-tutorial.sgml > x Data-Stag-0.11/homepage/images/ > x Data-Stag-0.11/homepage/images/k-schema-diagram.png > x Data-Stag-0.11/homepage/images/rr-schema-diagram.png > x Data-Stag-0.11/homepage/index.html > x Data-Stag-0.11/homepage/makefile > x Data-Stag-0.11/homepage/mk.sh > x Data-Stag-0.11/homepage/mkpodhtml.pl > x Data-Stag-0.11/homepage/mkscriptdoc.pl > x Data-Stag-0.11/homepage/script-docs/ > x Data-Stag-0.11/homepage/script-docs/selectall_html.html > x Data-Stag-0.11/homepage/script-docs/selectall_xml.html > x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html > x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html > x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html > x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html > x Data-Stag-0.11/homepage/script-docs/stag-db.html > x Data-Stag-0.11/homepage/script-docs/stag-diff.html > x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html > x Data-Stag-0.11/homepage/script-docs/stag-elcount.html > x Data-Stag-0.11/homepage/script-docs/stag-eval.html > x Data-Stag-0.11/homepage/script-docs/stag-filter.html > x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html > x Data-Stag-0.11/homepage/script-docs/stag-flatten.html > x Data-Stag-0.11/homepage/script-docs/stag-grep.html > x Data-Stag-0.11/homepage/script-docs/stag-handle.html > x Data-Stag-0.11/homepage/script-docs/stag-ir.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html > x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html > x Data-Stag-0.11/homepage/script-docs/stag-join.html > x Data-Stag-0.11/homepage/script-docs/stag-merge.html > x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html > x Data-Stag-0.11/homepage/script-docs/stag-parse.html > x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html > x Data-Stag-0.11/homepage/script-docs/stag-query.html > x Data-Stag-0.11/homepage/script-docs/stag-show-template.html > x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html > x Data-Stag-0.11/homepage/script-docs/stag-splitter.html > x Data-Stag-0.11/homepage/script-docs/stag-storenode.html > x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html > x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html > x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html > x Data-Stag-0.11/homepage/script-docs/stag-view.html > x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html > x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html > x Data-Stag-0.11/homepage/script-list.html > x Data-Stag-0.11/homepage/stag-db-tutorial.html > x Data-Stag-0.11/homepage/stag-poster.html > x Data-Stag-0.11/INSTALL > x Data-Stag-0.11/Makefile.PL > x Data-Stag-0.11/MANIFEST > x Data-Stag-0.11/META.yml > x Data-Stag-0.11/README > x Data-Stag-0.11/scripts/ > x Data-Stag-0.11/scripts/stag-autoschema.pl > x Data-Stag-0.11/scripts/stag-db.pl > x Data-Stag-0.11/scripts/stag-diff.pl > x Data-Stag-0.11/scripts/stag-drawtree.pl > x Data-Stag-0.11/scripts/stag-elcount.pl > x Data-Stag-0.11/scripts/stag-eval.pl > x Data-Stag-0.11/scripts/stag-filter.pl > x Data-Stag-0.11/scripts/stag-findsubtree.pl > x Data-Stag-0.11/scripts/stag-flatten.pl > x Data-Stag-0.11/scripts/stag-grep.pl > x Data-Stag-0.11/scripts/stag-handle.pl > x Data-Stag-0.11/scripts/stag-itext2simple.pl > x Data-Stag-0.11/scripts/stag-itext2sxpr.pl > x Data-Stag-0.11/scripts/stag-itext2xml.pl > x Data-Stag-0.11/scripts/stag-join.pl > x Data-Stag-0.11/scripts/stag-merge.pl > x Data-Stag-0.11/scripts/stag-mogrify.pl > x Data-Stag-0.11/scripts/stag-parse.pl > x Data-Stag-0.11/scripts/stag-query.pl > x Data-Stag-0.11/scripts/stag-splitter.pl > x Data-Stag-0.11/scripts/stag-view.pl > x Data-Stag-0.11/scripts/stag-xml2itext.pl > x Data-Stag-0.11/scripts/stag-xmlsplit.pl > x Data-Stag-0.11/t/ > x Data-Stag-0.11/t/animal.x > x Data-Stag-0.11/t/autoschema.t > x Data-Stag-0.11/t/barfly.x > x Data-Stag-0.11/t/bio.x > x Data-Stag-0.11/t/chainhandler.t > x Data-Stag-0.11/t/collapse.x > x Data-Stag-0.11/t/data/ > x Data-Stag-0.11/t/data/attrs.xml > x Data-Stag-0.11/t/data/bf.txt > x Data-Stag-0.11/t/data/eco.el > x Data-Stag-0.11/t/data/eco.itext > x Data-Stag-0.11/t/data/homol.itext > x Data-Stag-0.11/t/data/persons.el > x Data-Stag-0.11/t/db.t > x Data-Stag-0.11/t/emptytag.t > x Data-Stag-0.11/t/get.t > x Data-Stag-0.11/t/graph.x > x Data-Stag-0.11/t/handlers.t > x Data-Stag-0.11/t/handlers2.t > x Data-Stag-0.11/t/handlers2.x > x Data-Stag-0.11/t/hashdb.t > x Data-Stag-0.11/t/hashdb.x > x Data-Stag-0.11/t/homol.t > x Data-Stag-0.11/t/lisp.x > x Data-Stag-0.11/t/parsestr.t > x Data-Stag-0.11/t/path.x > x Data-Stag-0.11/t/path2.x > x Data-Stag-0.11/t/qmatch.t > x Data-Stag-0.11/t/roundtrip-attrs.t > x Data-Stag-0.11/t/set-attrs.t > x Data-Stag-0.11/t/set.t > x Data-Stag-0.11/t/sxpr.t > x Data-Stag-0.11/t/unhash.t > x Data-Stag-0.11/t/unset.t > x Data-Stag-0.11/t/write.t > x Data-Stag-0.11/t/xml1.t > x Data-Stag-0.11/t/xml2.t > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz > > > External Module XML::LibXSLT, XSLT, > is not installed on this computer. > Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations > > External Module XML::Parser::PerlSAX, SAX Handler, > is not installed on this computer. > Data::Stag::XMLParser in Data::Stag needs it for parsing XML > > External Module GD, Graphical Drawing Toolkit, > is not installed on this computer. > stag-drawtree.pl in Data::Stag needs it for drawing trees > > External Module Graph::Directed, Generic Graph data stucture and algorithms, > is not installed on this computer. > Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs > > External Module Tk, Tk, > is not installed on this computer. > stag-view.pl in Data::Stag needs it for tree viewer > > > Information: > > There are some external packages and perl modules, listed above, which > stag uses. This only effects the functionality which is listed above: > the rest of stag will work fine, which includes nearly all of the > core functionality. > > Enjoy the rest of stag, which you can use after going 'make install' > > Checking if your kit is complete... > Looks good > Writing Makefile for Data > Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites > cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm > cp Data/Stag.pm blib/lib/Data/Stag.pm > cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm > cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm > cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm > cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm > cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm > cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm > cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm > cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm > cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm > cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm > cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm > cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm > cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm > cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm > cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm > cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm > cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm > cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm > cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm > cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm > cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm > cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm > cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm > cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm > cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm > cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm > cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm > cp scripts/stag-view.pl blib/script/stag-view.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl > cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl > cp scripts/stag-grep.pl blib/script/stag-grep.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl > cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl > cp scripts/stag-merge.pl blib/script/stag-merge.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl > cp scripts/stag-parse.pl blib/script/stag-parse.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl > cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl > cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl > cp scripts/stag-join.pl blib/script/stag-join.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl > cp scripts/stag-db.pl blib/script/stag-db.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl > cp scripts/stag-filter.pl blib/script/stag-filter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl > cp scripts/stag-handle.pl blib/script/stag-handle.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl > cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl > cp scripts/stag-query.pl blib/script/stag-query.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl > cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl > cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl > cp scripts/stag-flatten.pl blib/script/stag-flatten.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl > cp scripts/stag-splitter.pl blib/script/stag-splitter.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl > cp scripts/stag-diff.pl blib/script/stag-diff.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl > cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl > /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl > Manifying blib/man1/stag-view.pl.1 > Manifying blib/man1/stag-mogrify.pl.1 > Manifying blib/man1/stag-grep.pl.1 > Manifying blib/man1/stag-handle.pl.1 > Manifying blib/man1/stag-drawtree.pl.1 > Manifying blib/man1/stag-query.pl.1 > Manifying blib/man1/stag-merge.pl.1 > Manifying blib/man1/stag-parse.pl.1 > Manifying blib/man1/stag-findsubtree.pl.1 > Manifying blib/man1/stag-join.pl.1 > Manifying blib/man1/stag-autoschema.pl.1 > Manifying blib/man1/stag-db.pl.1 > Manifying blib/man1/stag-flatten.pl.1 > Manifying blib/man1/stag-splitter.pl.1 > Manifying blib/man1/stag-diff.pl.1 > Manifying blib/man1/stag-filter.pl.1 > Manifying blib/man3/Data::Stag::StagDB.3pm > Manifying blib/man3/Data::Stag::SxprWriter.3pm > Manifying blib/man3/Data::Stag.3pm > Manifying blib/man3/Data::Stag::ChainHandler.3pm > Manifying blib/man3/Data::Stag::IndentParser.3pm > Manifying blib/man3/Data::Stag::Simple.3pm > Manifying blib/man3/Data::Stag::SAX2Stag.3pm > Manifying blib/man3/Data::Stag::Arr2HTML.3pm > Manifying blib/man3/Data::Stag::XSLHandler.3pm > Manifying blib/man3/Data::Stag::PerlWriter.3pm > Manifying blib/man3/Data::Stag::XSLTHandler.3pm > Manifying blib/man3/Data::Stag::DTDWriter.3pm > Manifying blib/man3/Data::Stag::Writer.3pm > Manifying blib/man3/Data::Stag::XMLWriter.3pm > Manifying blib/man3/Data::Stag::GraphHandler.3pm > Manifying blib/man3/Data::Stag::XMLParser.3pm > Manifying blib/man3/Data::Stag::StagImpl.3pm > Manifying blib/man3/Data::Stag::PodParser.3pm > Manifying blib/man3/Data::Stag::BaseGenerator.3pm > Manifying blib/man3/Data::Stag::IndentWriter.3pm > Manifying blib/man3/Data::Stag::HashDB.3pm > Manifying blib/man3/Data::Stag::null.3pm > Manifying blib/man3/Data::Stag::ITextParser.3pm > Manifying blib/man3/Data::Stag::BaseHandler.3pm > Manifying blib/man3/Data::Stag::ITextWriter.3pm > Manifying blib/man3/Data::Stag::SxprParser.3pm > CMUNGALL/Data-Stag-0.11.tar.gz > make -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/autoschema.........ok > t/chainhandler.......ok > t/db.................ok > t/emptytag...........ok > 3/3 skipped: various reasons > t/get................ok > t/handlers...........ok > t/handlers2..........ok > 1/9 skipped: various reasons > t/hashdb.............ok > t/homol..............ok > t/parsestr...........ok > 6/6 skipped: various reasons > t/qmatch.............ok > t/roundtrip-attrs....ok > 5/5 skipped: various reasons > t/set-attrs..........ok > 3/3 skipped: various reasons > t/set................ok > t/sxpr...............ok > t/unhash.............ok > t/unset..............ok > t/write..............ok > t/xml1...............ok > 7/7 skipped: various reasons > t/xml2...............ok > 4/4 skipped: various reasons > All tests successful, 29 subtests skipped. > Files=20, Tests=102, 1 wallclock secs ( 1.17 cusr + 0.23 csys = 1.40 CPU) > CMUNGALL/Data-Stag-0.11.tar.gz > make test -- OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > Running make install > Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at -e line 1 > make: *** [pure_site_install] Error 13 > CMUNGALL/Data-Stag-0.11.tar.gz > make install -- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store persistent state > > > *** (back in Bioperl Build.PL) *** > Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n > - ERROR: You chose to install Data::Stag but it failed to install > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) > * Optional prerequisite Spreadsheet::ParseExcel is not installed > (wanted for parsing Excel files, used by Bio::SeqIO::excel) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite Graph is not installed > (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) > * Optional prerequisite SVG::Graph is not installed > (wanted for creating SVG images, used by Bio::TreeIO::svggraph) > * Optional prerequisite SOAP::Lite is not installed > (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) > * Optional prerequisite Bio::ASN1::EntrezGene is not installed > (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Convert::Binary::C is not installed > (wanted for strider functionality, used by Bio::SeqIO::strider) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite XML::Twig is not installed > (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) > * Optional prerequisite Set::Scalar is not installed > (wanted for proper operation, used by Bio::Tree::Compatible) > * Optional prerequisite XML::Parser::PerlSAX is not installed > (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) > * Optional prerequisite XML::SAX::Writer is not installed > (wanted for writing xml, used by Bio::SeqIO::tigrxml) > * Optional prerequisite Clone is not installed > (wanted for cloning objects, used by Bio::Tools::Primer3) > * Optional prerequisite XML::DOM::XPath is not installed > (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) > * Optional prerequisite PostScript::TextBlock is not installed > (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions > of the modules indicated above before proceeding with this installation > > Checking features: > BioDBGFF.................disabled > * MySQL, Pg nor Oracle DBI drivers are installed > BioDBSeqFeature_mysql....disabled > - DBD::mysql is not installed > Network..................enabled > BioDBSeqFeature_BDB......enabled > > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] > - will install all scripts > > Do you want to run tests that require connection to servers across the internet > (likely to cause some failures)? y/n [n] n > - will not run internet-requiring tests > Deleting Build > Removed previous script 'Build' > > Creating new 'Build' script for 'BioPerl' version '1.006000' > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > t/Align/AlignStats...........................ok > t/Align/AlignUtil............................ok > t/Align/SimpleAlign..........................ok > t/Align/TreeBuild............................ok > t/Align/Utilities............................ok > t/AlignIO/AlignIO............................ok 1/28 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 > STACK: t/AlignIO/AlignIO.t:51 > ----------------------------------------------------------- > # Looks like you planned 28 tests but only ran 7. > # Looks like your test died just after 7. > t/AlignIO/AlignIO............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 8-28 > Failed 21/28 tests, 25.00% okay > t/AlignIO/arp................................ok 1/48 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. > Compilation failed in require at Bio/Root/Root.pm line 420, line 86. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 > STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 > STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 > STACK: t/AlignIO/arp.t:25 > ----------------------------------------------------------- > # Looks like you planned 48 tests but only ran 2. > # Looks like your test died just after 2. > t/AlignIO/arp................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-48 > Failed 46/48 tests, 4.17% okay > 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......................ok 1/159 > # Failed test 'use Bio::Annotation::TagTree;' > # at t/Annotation/Annotation.t line 20. > # Tried to use 'Bio::Annotation::TagTree'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. > # Compilation failed in require at (eval 37) line 2. > # BEGIN failed--compilation aborted at (eval 37) line 2. > t/Annotation/Annotation......................NOK 9/159 > # Failed test 'default itext' > # at t/Annotation/Annotation.t line 307. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > > # Failed test 'itext' > # at t/Annotation/Annotation.t line 315. > # 'ARRAY(0x100c02a48)' > # doesn't match '(?-xism:Name: CALM1)' > Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. > # Looks like you planned 159 tests but only ran 119. > # Looks like you failed 3 tests of 119 run. > # Looks like your test died just after 119. > t/Annotation/Annotation......................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 9, 117, 119-159 > Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................ok 1/51 > # Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > 1/24 skipped: various reasons > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/ClusterIO/ClusterIO........................ok > 8/12 skipped: various reasons > t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/ClusterIO/SequenceFamily.t:16 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. > # Looks like you planned 19 tests but only ran 2. > # Looks like your test died just after 2. > t/ClusterIO/SequenceFamily...................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 3-19 > Failed 17/19 tests, 10.53% okay > 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 > 11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 > STACK: t/LocalDB/Flat.t:89 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. > # Looks like you planned 24 tests but only ran 14. > # Looks like your test died just after 14. > t/LocalDB/Flat...............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 15-24 > Failed 10/24 tests, 58.33% okay > t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 > STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 > STACK: t/LocalDB/Index.t:91 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. > # Looks like you planned 64 tests but only ran 31. > # Looks like your test died just after 31. > t/LocalDB/Index..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 32-64 > Failed 33/64 tests, 48.44% okay > t/LocalDB/Registry...........................ok > 9/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > 19/267 skipped: various reasons > 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 > 10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/GraphAdaptor......................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/go.............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/IO/interpro.......................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/Ontology/IO/obo............................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Ontology..........................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/OntologyEngine....................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/OntologyStore.....................skipped > all skipped: The optional module Graph (or dependencies thereof) was not installed > t/Ontology/Relationship......................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/RelationshipType..................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Ontology/Term..............................skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Perl.......................................ok > 10/29 skipped: various reasons > 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..................................ok > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > 4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > 14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/HIV/HIV...........................ok > 13/30 skipped: various reasons > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................ok > 10/41 skipped: various reasons > t/RemoteDB/HIV/HIVQueryHelper................ok > t/RemoteDB/RefSeq............................ok > 10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > 8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................skipped > all skipped: The optional module XML::Twig (or dependencies thereof) was not installed > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > t/Restriction/IO.............................ok 1/18 > # Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > 3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > 2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > all 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.............................ok 1/1093 > # Failed (TODO) test at t/SearchIO/blast.t line 527. > # '0.852' > # > > # '0.9' > > # Failed (TODO) test at t/SearchIO/blast.t line 528. > # '1.599' > # <= > # '1' > t/SearchIO/blast.............................ok > t/SearchIO/blast_pull........................ok 1/289 > # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # got: '0.946' > # expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > t/SearchIO/blastxml..........................ok 1/298 > # Failed (TODO) test at t/SearchIO/blastxml.t line 258. > # got: undef > # expected: '31984247' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 259. > # got: undef > # expected: '88780' > > # Failed (TODO) test at t/SearchIO/blastxml.t line 260. > # got: undef > # expected: '49' > t/SearchIO/blastxml..........................ok > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > 4/45 skipped: various reasons > 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...........................ok 1/116 > # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # got: 'Bio::Location::Simple=HASH(0x100838ce8)' > # expected: undef > > # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # got: '\-\.=~' > # expected: '-\?' > > # Failed (TODO) test at t/Seq/LocatableSeq.t 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 > all 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 > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > 7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. > Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. > BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqIO/Handler.t:20 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. > # Looks like you planned 550 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/Handler..............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-550 > Failed 549/550 tests, 0.18% okay > t/SeqIO/MultiFile............................ok > t/SeqIO/Multiple_fasta.......................ok > t/SeqIO/SeqBuilder...........................ok > t/SeqIO/Splicedseq...........................ok > t/SeqIO/abi..................................skipped > all 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..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................skipped > all skipped: The optional module XML::DOM (or dependencies thereof) was not installed > t/SeqIO/bsml_sax.............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ > # Failed test 'use Bio::SeqIO::chaos;' > # at t/SeqIO/chaos.t line 15. > # Tried to use 'Bio::SeqIO::chaos'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. > # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > # Looks like you failed 1 test of 8. > t/SeqIO/chaos................................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED test 1 > Failed 1/8 tests, 87.50% okay > t/SeqIO/chaosxml.............................skipped > all skipped: The optional module Data::Stag (or dependencies thereof) was not installed > t/SeqIO/ctf..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................skipped > all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed > t/SeqIO/excel................................skipped > all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed > t/SeqIO/exp..................................skipped > all 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 > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/gcg..................................ok 1/17 > # Failed (TODO) test 'primary_id' > # at t/SeqIO/gcg.t line 54. > # got: 'Bio::PrimarySeq=HASH(0x100830bd0)' > # expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................skipped > all 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 > all 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 > all 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..................................ok 1/59 > # Failed (TODO) test 'accuracies' > # at t/SeqIO/scf.t line 78. > # got: 'ARRAY(0x100ac5648)' > # expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................skipped > all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss................................ > # Failed test 'use Bio::SeqIO::swiss;' > # at t/SeqIO/swiss.t line 12. > # Tried to use 'Bio::SeqIO::swiss'. > # Error: Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. > # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > # Compilation failed in require at (eval 14) line 2. > # BEGIN failed--compilation aborted at (eval 14) line 2. > Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. > # Looks like you planned 240 tests but only ran 1. > # Looks like you failed 1 test of 1 run. > # Looks like your test died just after 1. > t/SeqIO/swiss................................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-240 > Failed 240/240 tests, 0.00% okay > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > 112/450 skipped: various reasons > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................skipped > all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq..............................skipped > all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed > t/SeqIO/ztr..................................skipped > all 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 1/49Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/SeqTools/GuessSeqFormat.t:62 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > t/SeqTools/GuessSeqFormat....................NOK 25/49 > # Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. > # ' > # at t/SeqTools/GuessSeqFormat.t line 71. > # got: '0' > # expected: '1' > # Looks like you planned 49 tests but ran 1 extra. > # Looks like you failed 1 test of 50 run. > t/SeqTools/GuessSeqFormat....................dubious > Test returned status 1 (wstat 256, 0x100) > DIED. FAILED tests 25, 50 > Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) > t/SeqTools/OddCodes..........................ok > t/SeqTools/SeqPattern........................ok > t/SeqTools/SeqStats..........................ok > t/SeqTools/SeqUtils..........................ok > t/SeqTools/SeqWords..........................ok > t/Species....................................ok > 5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > all 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 > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found > Exception > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. > BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. > Compilation failed in require at Bio/SeqIO/swiss.pm line 197. > BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. > Compilation failed in require at Bio/Root/Root.pm line 420. > > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 > STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 > STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 > STACK: t/Tools/Analysis/Protein/Scansite.t:23 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run time > Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. > # Looks like you planned 14 tests but only ran 4. > # Looks like your test died just after 4. > t/Tools/Analysis/Protein/Scansite............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 5-14 > Failed 10/14 tests, 28.57% okay > t/Tools/Analysis/Protein/Sopma...............ok > 12/16 skipped: various reasons > 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 > all 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......................skipped > all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > 12/45 skipped: various reasons > 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 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 > all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/GraphViz.................skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............skipped > all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/RandomFactory............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............skipped > all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed > t/Tree/RandomTreeFactory.....................ok > t/Tree/Tree..................................ok > t/Tree/TreeIO................................ok > 2/74 skipped: various reasons > t/Tree/TreeIO/lintree........................ok > t/Tree/TreeIO/newick.........................ok > t/Tree/TreeIO/nexus..........................ok > t/Tree/TreeIO/nhx............................ok > t/Tree/TreeIO/phyloxml.......................ok > t/Tree/TreeIO/svggraph.......................ok > 3/4 skipped: various reasons > 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 > 15/26 skipped: various reasons > Failed Test Stat Wstat Total Fail List of Failed > ------------------------------------------------------------------------------- > t/AlignIO/AlignIO.t 255 65280 28 42 8-28 > t/AlignIO/arp.t 255 65280 48 92 3-48 > t/Annotation/Annotation.t 255 65280 159 83 9 117 119-159 > t/ClusterIO/SequenceFamily.t 255 65280 19 34 3-19 > t/LocalDB/Flat.t 255 65280 24 20 15-24 > t/LocalDB/Index.t 255 65280 64 66 32-64 > t/SeqIO/Handler.t 255 65280 550 1098 2-550 > t/SeqIO/chaos.t 1 256 8 1 1 > t/SeqIO/swiss.t 255 65280 240 479 1-240 > t/SeqTools/GuessSeqFormat.t 1 256 49 2 25 50 > t/Tools/Analysis/Protein/Scansite.t 255 65280 14 20 5-14 > 57 tests and 313 subtests skipped. > Failed 11/318 test scripts. 970/17228 subtests failed. > Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) > Failed 11/318 test programs. 970/17228 subtests failed. > Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install > Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS > Deleting blib/script/bp_sreformat.PLS.bak > blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl > Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS > Deleting blib/script/seqconvert.PLS.bak > blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl > Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS > Deleting blib/script/parse_hmmsearch.PLS.bak > blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl > Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS > Deleting blib/script/bp_seqret.PLS.bak > blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl > Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS > Deleting blib/script/tree2pag.PLS.bak > blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl > Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS > Deleting blib/script/meta_gff.PLS.bak > blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl > Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS > Deleting blib/script/nexus2nh.PLS.bak > blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl > Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS > Deleting blib/script/filter_search.PLS.bak > blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS > blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl > Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS > Deleting blib/script/generate_histogram.PLS.bak > blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl > Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS > Deleting blib/script/heterogeneity_test.PLS.bak > blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl > Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS > Deleting blib/script/flanks.PLS.bak > blib/script/flanks.PLS -> blib/script/bp_flanks.pl > Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS > Deleting blib/script/split_seq.PLS.bak > blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl > Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS > Deleting blib/script/load_gff.PLS.bak > blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl > Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS > Deleting blib/script/biogetseq.PLS.bak > blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl > Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS > Deleting blib/script/bp_fetch.PLS.bak > blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl > Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS > Deleting blib/script/mutate.PLS.bak > blib/script/mutate.PLS -> blib/script/bp_mutate.pl > Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS > Deleting blib/script/process_sgd.PLS.bak > blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl > Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS > Deleting blib/script/bp_index.PLS.bak > blib/script/bp_index.PLS -> blib/script/bp_index.pl > Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS > Deleting blib/script/dbsplit.PLS.bak > blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl > Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS > Deleting blib/script/oligo_count.PLS.bak > blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS > Deleting blib/script/bp_seqfeature_load.PLS.bak > blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl > Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS > Deleting blib/script/process_gadfly.PLS.bak > blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl > Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS > Deleting blib/script/hmmer_to_table.PLS.bak > blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl > Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS > Deleting blib/script/fastam9_to_table.PLS.bak > blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl > Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS > Deleting blib/script/biofetch_genbank_proxy.PLS.bak > blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl > Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS > Deleting blib/script/seq_length.PLS.bak > blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl > Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS > Deleting blib/script/extract_feature_seq.PLS.bak > blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl > Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS > Deleting blib/script/genbank2gff.PLS.bak > blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl > Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS > Deleting blib/script/taxid4species.PLS.bak > blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl > Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS > Deleting blib/script/bulk_load_gff.PLS.bak > blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl > Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS > Deleting blib/script/search2gff.PLS.bak > blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl > Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS > Deleting blib/script/blast2tree.PLS.bak > blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl > Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS > Deleting blib/script/make_mrna_protein.PLS.bak > blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl > Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS > Deleting blib/script/unflatten_seq.PLS.bak > blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl > Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS > Deleting blib/script/search2tribe.PLS.bak > blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl > Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS > Deleting blib/script/bioflat_index.PLS.bak > blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl > Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS > Deleting blib/script/bp_seqfeature_delete.PLS.bak > blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl > Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS > Deleting blib/script/query_entrez_taxa.PLS.bak > blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl > Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS > Deleting blib/script/pairwise_kaks.PLS.bak > blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl > Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS > Deleting blib/script/fast_load_gff.PLS.bak > blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl > Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS > Deleting blib/script/chaos_plot.PLS.bak > blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl > Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS > Deleting blib/script/taxonomy2tree.PLS.bak > blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl > Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS > Deleting blib/script/bp_mrtrans.PLS.bak > blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl > Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS > Deleting blib/script/search2alnblocks.PLS.bak > blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl > Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS > Deleting blib/script/download_query_genbank.PLS.bak > blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl > Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS > Deleting blib/script/bp_nrdb.PLS.bak > blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl > Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS > Deleting blib/script/mask_by_search.PLS.bak > blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl > Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS > Deleting blib/script/gccalc.PLS.bak > blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl > Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS > Deleting blib/script/composite_LD.PLS.bak > blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl > Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS > Deleting blib/script/classify_hits_kingdom.PLS.bak > blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl > Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS > Deleting blib/script/aacomp.PLS.bak > blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl > Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS > Deleting blib/script/process_wormbase.PLS.bak > blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl > Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS > Deleting blib/script/local_taxonomydb_query.PLS.bak > blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl > Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS > Deleting blib/script/biblio.PLS.bak > blib/script/biblio.PLS -> blib/script/bp_biblio.pl > Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS > Deleting blib/script/seqretsplit.PLS.bak > blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl > Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS > Deleting blib/script/remote_blast.PLS.bak > blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl > Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS > Deleting blib/script/genbank2gff3.PLS.bak > blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl > Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS > Deleting blib/script/search2table.PLS.bak > blib/script/search2table.PLS -> blib/script/bp_search2table.pl > Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS > Deleting blib/script/search2BSML.PLS.bak > blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl > Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS > Deleting blib/script/translate_seq.PLS.bak > blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl > Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 > Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 > Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 > Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 > Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 > Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 > Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 > Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 > Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 > Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 > Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 > Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 > Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 > Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 > Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 > Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 > Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 > Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 > Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 > Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 > Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 > Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 > Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 > Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 > Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 > Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 > Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 > Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 > Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 > Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 > Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 > Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 > Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 > Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 > Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 > Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 > Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 > Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 > Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 > Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 > Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 > Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 > Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 > Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 > Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 > Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 > Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 > Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 > Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 > Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 > Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 > Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 > Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 > Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 > Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 > Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 > Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 > Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From wkretzsch at gmail.com Fri Jul 30 15:37:08 2010 From: wkretzsch at gmail.com (Warren W. Kretzschmar) Date: Fri, 30 Jul 2010 11:37:08 -0400 Subject: [Bioperl-l] installing bioperl In-Reply-To: References: Message-ID: Alternatively I think you might have run "make install" when what you actually wanted to run was "sudo make install". The sudo means you install everything with root rights (which you say you have). It'll ask you for a password and then it will have the rights to install into /usr/local/bin Cheers, Warren On Fri, Jul 30, 2010 at 9:54 AM, Robson de Souza wrote: > Did you try, as root, > > ./Build.pl --install_base /opt/local > > ? > > Also, check the INSTALL file at the root of the bioperl distribution. > Robson > > On Fri, Jul 30, 2010 at 5:37 AM, Carrie O'Malley wrote: >> Hi there >> I'm trying to install bioperl, I have tried every possible option on your wiki page but failing. I have a macbook pro running 10.6.3. I have installed dev tools. I have become root. I have tried to install using Build.pl after downloading ?BioPerl-1.6.0.tar.gz as instructed, and failed. I have tried using cpan to install too. >> I am not able to complete the installation as every time I get: >> >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> ?I have tried using both methods to install into a local folder and get the same thing >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/home/users/carrieomalley/bin' >> mkdir /home/users: Operation not supported at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> I have made every possible folder write enabled. I have no idea what's going on. I'm not a programmer, as I'm sure if patently obvious, I'm just a phd student doing bioinformatics on my sequence data. I'm totally clueless. Any help would be much, much appreciated. >> >> >> If it helps, I've added the whole terminal output. Please help, I really need the Bioperl tools for my research :( >> >> >> Many thanks in advance >> Carrie >> >> >> >> >> >> Carrie-OMalleys-MacBook-Pro:~ carrieomalley$ cd BioPerl-1.6.0 >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ perl Build.PL >> Checking whether your kit is complete... >> Looks good >> >> Checking prerequisites... >> ?- ERROR: Data::Stag is not installed >> (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) >> CPAN: Storable loaded ok (v2.18) >> Going to read /Users/carrieomalley/.cpan/Metadata >> ?Database was generated on Sat, 10 Jul 2010 11:27:04 GMT >> Running install for module 'Data::Stag' >> 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/Users/carrieomalley/.cpan/prefs' >> Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /Users/carrieomalley/.cpan/sources/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok >> x Data-Stag-0.11/ >> x Data-Stag-0.11/c-ext/ >> x Data-Stag-0.11/c-ext/README.c-ext >> x Data-Stag-0.11/c-ext/staglib.c >> x Data-Stag-0.11/c-ext/staglib.h >> x Data-Stag-0.11/Changes >> x Data-Stag-0.11/Data/ >> x Data-Stag-0.11/Data/Stag/ >> x Data-Stag-0.11/Data/Stag/Arr2HTML.pm >> x Data-Stag-0.11/Data/Stag/Base.pm >> x Data-Stag-0.11/Data/Stag/BaseGenerator.pm >> x Data-Stag-0.11/Data/Stag/BaseHandler.pm >> x Data-Stag-0.11/Data/Stag/ChainHandler.pm >> x Data-Stag-0.11/Data/Stag/DTDWriter.pm >> x Data-Stag-0.11/Data/Stag/GraphHandler.pm >> x Data-Stag-0.11/Data/Stag/HashDB.pm >> x Data-Stag-0.11/Data/Stag/IndentParser.pm >> x Data-Stag-0.11/Data/Stag/IndentWriter.pm >> x Data-Stag-0.11/Data/Stag/ITextParser.pm >> x Data-Stag-0.11/Data/Stag/ITextWriter.pm >> x Data-Stag-0.11/Data/Stag/null.pm >> x Data-Stag-0.11/Data/Stag/PerlWriter.pm >> x Data-Stag-0.11/Data/Stag/PodParser.pm >> x Data-Stag-0.11/Data/Stag/SAX2Stag.pm >> x Data-Stag-0.11/Data/Stag/Simple.pm >> x Data-Stag-0.11/Data/Stag/StagDB.pm >> x Data-Stag-0.11/Data/Stag/StagI.pm >> x Data-Stag-0.11/Data/Stag/StagImpl.pm >> x Data-Stag-0.11/Data/Stag/SxprParser.pm >> x Data-Stag-0.11/Data/Stag/SxprWriter.pm >> x Data-Stag-0.11/Data/Stag/Util.pm >> x Data-Stag-0.11/Data/Stag/Writer.pm >> x Data-Stag-0.11/Data/Stag/XMLParser.pm >> x Data-Stag-0.11/Data/Stag/XMLWriter.pm >> x Data-Stag-0.11/Data/Stag/XSLHandler.pm >> x Data-Stag-0.11/Data/Stag/XSLTHandler.pm >> x Data-Stag-0.11/Data/Stag.pm >> x Data-Stag-0.11/dev/ >> x Data-Stag-0.11/dev/create-manifest.sh >> x Data-Stag-0.11/dev/data-stag.spec >> x Data-Stag-0.11/dev/mkspec.pl >> x Data-Stag-0.11/elisp/ >> x Data-Stag-0.11/elisp/itext-mode.el >> x Data-Stag-0.11/homepage/ >> x Data-Stag-0.11/homepage/archBIG.png >> x Data-Stag-0.11/homepage/dbstag-tutorial.sgml >> x Data-Stag-0.11/homepage/images/ >> x Data-Stag-0.11/homepage/images/k-schema-diagram.png >> x Data-Stag-0.11/homepage/images/rr-schema-diagram.png >> x Data-Stag-0.11/homepage/index.html >> x Data-Stag-0.11/homepage/makefile >> x Data-Stag-0.11/homepage/mk.sh >> x Data-Stag-0.11/homepage/mkpodhtml.pl >> x Data-Stag-0.11/homepage/mkscriptdoc.pl >> x Data-Stag-0.11/homepage/script-docs/ >> x Data-Stag-0.11/homepage/script-docs/selectall_html.html >> x Data-Stag-0.11/homepage/script-docs/selectall_xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoddl.html >> x Data-Stag-0.11/homepage/script-docs/stag-autoschema.html >> x Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html >> x Data-Stag-0.11/homepage/script-docs/stag-bulkload.html >> x Data-Stag-0.11/homepage/script-docs/stag-db.html >> x Data-Stag-0.11/homepage/script-docs/stag-diff.html >> x Data-Stag-0.11/homepage/script-docs/stag-drawtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-elcount.html >> x Data-Stag-0.11/homepage/script-docs/stag-eval.html >> x Data-Stag-0.11/homepage/script-docs/stag-filter.html >> x Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html >> x Data-Stag-0.11/homepage/script-docs/stag-flatten.html >> x Data-Stag-0.11/homepage/script-docs/stag-grep.html >> x Data-Stag-0.11/homepage/script-docs/stag-handle.html >> x Data-Stag-0.11/homepage/script-docs/stag-ir.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html >> x Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html >> x Data-Stag-0.11/homepage/script-docs/stag-join.html >> x Data-Stag-0.11/homepage/script-docs/stag-merge.html >> x Data-Stag-0.11/homepage/script-docs/stag-mogrify.html >> x Data-Stag-0.11/homepage/script-docs/stag-parse.html >> x Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html >> x Data-Stag-0.11/homepage/script-docs/stag-query.html >> x Data-Stag-0.11/homepage/script-docs/stag-show-template.html >> x Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html >> x Data-Stag-0.11/homepage/script-docs/stag-splitter.html >> x Data-Stag-0.11/homepage/script-docs/stag-storenode.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2bin.html >> x Data-Stag-0.11/homepage/script-docs/stag-template2pod.html >> x Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html >> x Data-Stag-0.11/homepage/script-docs/stag-view.html >> x Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html >> x Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html >> x Data-Stag-0.11/homepage/script-list.html >> x Data-Stag-0.11/homepage/stag-db-tutorial.html >> x Data-Stag-0.11/homepage/stag-poster.html >> x Data-Stag-0.11/INSTALL >> x Data-Stag-0.11/Makefile.PL >> x Data-Stag-0.11/MANIFEST >> x Data-Stag-0.11/META.yml >> x Data-Stag-0.11/README >> x Data-Stag-0.11/scripts/ >> x Data-Stag-0.11/scripts/stag-autoschema.pl >> x Data-Stag-0.11/scripts/stag-db.pl >> x Data-Stag-0.11/scripts/stag-diff.pl >> x Data-Stag-0.11/scripts/stag-drawtree.pl >> x Data-Stag-0.11/scripts/stag-elcount.pl >> x Data-Stag-0.11/scripts/stag-eval.pl >> x Data-Stag-0.11/scripts/stag-filter.pl >> x Data-Stag-0.11/scripts/stag-findsubtree.pl >> x Data-Stag-0.11/scripts/stag-flatten.pl >> x Data-Stag-0.11/scripts/stag-grep.pl >> x Data-Stag-0.11/scripts/stag-handle.pl >> x Data-Stag-0.11/scripts/stag-itext2simple.pl >> x Data-Stag-0.11/scripts/stag-itext2sxpr.pl >> x Data-Stag-0.11/scripts/stag-itext2xml.pl >> x Data-Stag-0.11/scripts/stag-join.pl >> x Data-Stag-0.11/scripts/stag-merge.pl >> x Data-Stag-0.11/scripts/stag-mogrify.pl >> x Data-Stag-0.11/scripts/stag-parse.pl >> x Data-Stag-0.11/scripts/stag-query.pl >> x Data-Stag-0.11/scripts/stag-splitter.pl >> x Data-Stag-0.11/scripts/stag-view.pl >> x Data-Stag-0.11/scripts/stag-xml2itext.pl >> x Data-Stag-0.11/scripts/stag-xmlsplit.pl >> x Data-Stag-0.11/t/ >> x Data-Stag-0.11/t/animal.x >> x Data-Stag-0.11/t/autoschema.t >> x Data-Stag-0.11/t/barfly.x >> x Data-Stag-0.11/t/bio.x >> x Data-Stag-0.11/t/chainhandler.t >> x Data-Stag-0.11/t/collapse.x >> x Data-Stag-0.11/t/data/ >> x Data-Stag-0.11/t/data/attrs.xml >> x Data-Stag-0.11/t/data/bf.txt >> x Data-Stag-0.11/t/data/eco.el >> x Data-Stag-0.11/t/data/eco.itext >> x Data-Stag-0.11/t/data/homol.itext >> x Data-Stag-0.11/t/data/persons.el >> x Data-Stag-0.11/t/db.t >> x Data-Stag-0.11/t/emptytag.t >> x Data-Stag-0.11/t/get.t >> x Data-Stag-0.11/t/graph.x >> x Data-Stag-0.11/t/handlers.t >> x Data-Stag-0.11/t/handlers2.t >> x Data-Stag-0.11/t/handlers2.x >> x Data-Stag-0.11/t/hashdb.t >> x Data-Stag-0.11/t/hashdb.x >> x Data-Stag-0.11/t/homol.t >> x Data-Stag-0.11/t/lisp.x >> x Data-Stag-0.11/t/parsestr.t >> x Data-Stag-0.11/t/path.x >> x Data-Stag-0.11/t/path2.x >> x Data-Stag-0.11/t/qmatch.t >> x Data-Stag-0.11/t/roundtrip-attrs.t >> x Data-Stag-0.11/t/set-attrs.t >> x Data-Stag-0.11/t/set.t >> x Data-Stag-0.11/t/sxpr.t >> x Data-Stag-0.11/t/unhash.t >> x Data-Stag-0.11/t/unset.t >> x Data-Stag-0.11/t/write.t >> x Data-Stag-0.11/t/xml1.t >> x Data-Stag-0.11/t/xml2.t >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> ?CPAN.pm: Going to build C/CM/CMUNGALL/Data-Stag-0.11.tar.gz >> >> >> External Module XML::LibXSLT, XSLT, >> ?is not installed on this computer. >> ?Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations >> >> External Module XML::Parser::PerlSAX, SAX Handler, >> ?is not installed on this computer. >> ?Data::Stag::XMLParser in Data::Stag needs it for parsing XML >> >> External Module GD, Graphical Drawing Toolkit, >> ?is not installed on this computer. >> ?stag-drawtree.pl in Data::Stag needs it for drawing trees >> >> External Module Graph::Directed, Generic Graph data stucture and algorithms, >> ?is not installed on this computer. >> ?Data::Stag::GraphHandler in Data::Stag needs it for transforming stag trees to graphs >> >> External Module Tk, Tk, >> ?is not installed on this computer. >> ?stag-view.pl in Data::Stag needs it for tree viewer >> >> >> Information: >> >> ? There are some external packages and perl modules, listed above, which >> ? stag uses. This only effects the functionality which is listed above: >> ? the rest of stag will work fine, which includes nearly all of the >> ? core functionality. >> >> ? Enjoy the rest of stag, which you can use after going 'make install' >> >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Data >> Could not read '/Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/META.yml'. Falling back to other methods to determine prerequisites >> cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm >> cp Data/Stag.pm blib/lib/Data/Stag.pm >> cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm >> cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm >> cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm >> cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm >> cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm >> cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm >> cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm >> cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm >> cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm >> cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm >> cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm >> cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm >> cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm >> cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm >> cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm >> cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm >> cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm >> cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm >> cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm >> cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm >> cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm >> cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm >> cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm >> cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm >> cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm >> cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm >> cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm >> cp scripts/stag-view.pl blib/script/stag-view.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-view.pl >> cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-mogrify.pl >> cp scripts/stag-grep.pl blib/script/stag-grep.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-grep.pl >> cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-xml2itext.pl >> cp scripts/stag-merge.pl blib/script/stag-merge.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-merge.pl >> cp scripts/stag-parse.pl blib/script/stag-parse.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-parse.pl >> cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2sxpr.pl >> cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2simple.pl >> cp scripts/stag-join.pl blib/script/stag-join.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-join.pl >> cp scripts/stag-db.pl blib/script/stag-db.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-db.pl >> cp scripts/stag-filter.pl blib/script/stag-filter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-filter.pl >> cp scripts/stag-handle.pl blib/script/stag-handle.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-handle.pl >> cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-drawtree.pl >> cp scripts/stag-query.pl blib/script/stag-query.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-query.pl >> cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-findsubtree.pl >> cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-autoschema.pl >> cp scripts/stag-flatten.pl blib/script/stag-flatten.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-flatten.pl >> cp scripts/stag-splitter.pl blib/script/stag-splitter.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-splitter.pl >> cp scripts/stag-diff.pl blib/script/stag-diff.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-diff.pl >> cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl >> /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/stag-itext2xml.pl >> Manifying blib/man1/stag-view.pl.1 >> Manifying blib/man1/stag-mogrify.pl.1 >> Manifying blib/man1/stag-grep.pl.1 >> Manifying blib/man1/stag-handle.pl.1 >> Manifying blib/man1/stag-drawtree.pl.1 >> Manifying blib/man1/stag-query.pl.1 >> Manifying blib/man1/stag-merge.pl.1 >> Manifying blib/man1/stag-parse.pl.1 >> Manifying blib/man1/stag-findsubtree.pl.1 >> Manifying blib/man1/stag-join.pl.1 >> Manifying blib/man1/stag-autoschema.pl.1 >> Manifying blib/man1/stag-db.pl.1 >> Manifying blib/man1/stag-flatten.pl.1 >> Manifying blib/man1/stag-splitter.pl.1 >> Manifying blib/man1/stag-diff.pl.1 >> Manifying blib/man1/stag-filter.pl.1 >> Manifying blib/man3/Data::Stag::StagDB.3pm >> Manifying blib/man3/Data::Stag::SxprWriter.3pm >> Manifying blib/man3/Data::Stag.3pm >> Manifying blib/man3/Data::Stag::ChainHandler.3pm >> Manifying blib/man3/Data::Stag::IndentParser.3pm >> Manifying blib/man3/Data::Stag::Simple.3pm >> Manifying blib/man3/Data::Stag::SAX2Stag.3pm >> Manifying blib/man3/Data::Stag::Arr2HTML.3pm >> Manifying blib/man3/Data::Stag::XSLHandler.3pm >> Manifying blib/man3/Data::Stag::PerlWriter.3pm >> Manifying blib/man3/Data::Stag::XSLTHandler.3pm >> Manifying blib/man3/Data::Stag::DTDWriter.3pm >> Manifying blib/man3/Data::Stag::Writer.3pm >> Manifying blib/man3/Data::Stag::XMLWriter.3pm >> Manifying blib/man3/Data::Stag::GraphHandler.3pm >> Manifying blib/man3/Data::Stag::XMLParser.3pm >> Manifying blib/man3/Data::Stag::StagImpl.3pm >> Manifying blib/man3/Data::Stag::PodParser.3pm >> Manifying blib/man3/Data::Stag::BaseGenerator.3pm >> Manifying blib/man3/Data::Stag::IndentWriter.3pm >> Manifying blib/man3/Data::Stag::HashDB.3pm >> Manifying blib/man3/Data::Stag::null.3pm >> Manifying blib/man3/Data::Stag::ITextParser.3pm >> Manifying blib/man3/Data::Stag::BaseHandler.3pm >> Manifying blib/man3/Data::Stag::ITextWriter.3pm >> Manifying blib/man3/Data::Stag::SxprParser.3pm >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/autoschema.........ok >> t/chainhandler.......ok >> t/db.................ok >> t/emptytag...........ok >> ? ? ? ?3/3 skipped: various reasons >> t/get................ok >> t/handlers...........ok >> t/handlers2..........ok >> ? ? ? ?1/9 skipped: various reasons >> t/hashdb.............ok >> t/homol..............ok >> t/parsestr...........ok >> ? ? ? ?6/6 skipped: various reasons >> t/qmatch.............ok >> t/roundtrip-attrs....ok >> ? ? ? ?5/5 skipped: various reasons >> t/set-attrs..........ok >> ? ? ? ?3/3 skipped: various reasons >> t/set................ok >> t/sxpr...............ok >> t/unhash.............ok >> t/unset..............ok >> t/write..............ok >> t/xml1...............ok >> ? ? ? ?7/7 skipped: various reasons >> t/xml2...............ok >> ? ? ? ?4/4 skipped: various reasons >> All tests successful, 29 subtests skipped. >> Files=20, Tests=102, ?1 wallclock secs ( 1.17 cusr + ?0.23 csys = ?1.40 CPU) >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make test -- OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> Running make install >> Prepending /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/arch /Users/carrieomalley/.cpan/build/Data-Stag-0.11-Zb1gaN/blib/lib to PERL5LIB for 'install' >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at -e line 1 >> make: *** [pure_site_install] Error 13 >> ?CMUNGALL/Data-Stag-0.11.tar.gz >> ?make install ?-- NOT OK >> Warning (usually harmless): 'YAML' not installed, will not store persistent state >> >> >> *** (back in Bioperl Build.PL) *** >> Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] n >> ?- ERROR: You chose to install Data::Stag but it failed to install >> ?* Optional prerequisite Ace is not installed >> ? (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) >> ?* Optional prerequisite Spreadsheet::ParseExcel is not installed >> ? (wanted for parsing Excel files, used by Bio::SeqIO::excel) >> ?* Optional prerequisite Math::Random is not installed >> ? (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) >> ?* Optional prerequisite Graph is not installed >> ? (wanted for ontology engine implementation for the GO parser, used by Bio::PhyloNetwork) >> ?* Optional prerequisite SVG::Graph is not installed >> ? (wanted for creating SVG images, used by Bio::TreeIO::svggraph) >> ?* Optional prerequisite SOAP::Lite is not installed >> ? (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap) >> ?* Optional prerequisite Bio::ASN1::EntrezGene is not installed >> ? (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) >> ?* Optional prerequisite GraphViz is not installed >> ? (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) >> ?* Optional prerequisite Array::Compare is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite Convert::Binary::C is not installed >> ? (wanted for strider functionality, used by Bio::SeqIO::strider) >> ?* Optional prerequisite Algorithm::Munkres is not installed >> ? (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) >> ?* Optional prerequisite XML::Twig is not installed >> ? (wanted for parsing xml, used by Bio::Variation::IO::xml, Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils) >> ?* Optional prerequisite Set::Scalar is not installed >> ? (wanted for proper operation, used by Bio::Tree::Compatible) >> ?* Optional prerequisite XML::Parser::PerlSAX is not installed >> ? (wanted for parsing xml, used by Bio::SeqIO::tinyseq, Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and Bio::ClusterIO::dbsnp) >> ?* Optional prerequisite XML::SAX::Writer is not installed >> ? (wanted for writing xml, used by Bio::SeqIO::tigrxml) >> ?* Optional prerequisite Clone is not installed >> ? (wanted for cloning objects, used by Bio::Tools::Primer3) >> ?* Optional prerequisite XML::DOM::XPath is not installed >> ? (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) >> ?* Optional prerequisite PostScript::TextBlock is not installed >> ? (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) >> >> ERRORS/WARNINGS FOUND IN PREREQUISITES. ?You may wish to install the versions >> of the modules indicated above before proceeding with this installation >> >> Checking features: >> ?BioDBGFF.................disabled >> ? ?* MySQL, Pg nor Oracle DBI drivers are installed >> ?BioDBSeqFeature_mysql....disabled >> ? ?- DBD::mysql is not installed >> ?Network..................enabled >> ?BioDBSeqFeature_BDB......enabled >> >> Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] >> ?- will install all scripts >> >> Do you want to run tests that require connection to servers across the internet >> (likely to cause some failures)? y/n [n] n >> ?- will not run internet-requiring tests >> Deleting Build >> Removed previous script 'Build' >> >> Creating new 'Build' script for 'BioPerl' version '1.006000' >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build test >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> t/Align/AlignStats...........................ok >> t/Align/AlignUtil............................ok >> t/Align/SimpleAlign..........................ok >> t/Align/TreeBuild............................ok >> t/Align/Utilities............................ok >> t/AlignIO/AlignIO............................ok 1/28 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: Bio::AlignIO::READLINE Bio/AlignIO.pm:484 >> STACK: t/AlignIO/AlignIO.t:51 >> ----------------------------------------------------------- >> # Looks like you planned 28 tests but only ran 7. >> # Looks like your test died just after 7. >> t/AlignIO/AlignIO............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 8-28 >> ? ? ? ?Failed 21/28 tests, 25.00% okay >> t/AlignIO/arp................................ok 1/48 >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Annotation class 'Bio::Annotation::TagTree' failed to load: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::Annotation::TagTree. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112, line 86. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112, line 86. >> Compilation failed in require at Bio/Root/Root.pm line 420, line 86. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:183 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Annotation::AnnotationFactory::type Bio/Annotation/AnnotationFactory.pm:185 >> STACK: Bio::AlignIO::arp::_process_annotation Bio/AlignIO/arp.pm:216 >> STACK: Bio::AlignIO::arp::next_aln Bio/AlignIO/arp.pm:137 >> STACK: t/AlignIO/arp.t:25 >> ----------------------------------------------------------- >> # Looks like you planned 48 tests but only ran 2. >> # Looks like your test died just after 2. >> t/AlignIO/arp................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-48 >> ? ? ? ?Failed 46/48 tests, 4.17% okay >> 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......................ok 1/159 >> # ? Failed test 'use Bio::Annotation::TagTree;' >> # ? at t/Annotation/Annotation.t line 20. >> # ? ? Tried to use 'Bio::Annotation::TagTree'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/Annotation/Annotation.t line 20. >> # Compilation failed in require at (eval 37) line 2. >> # BEGIN failed--compilation aborted at (eval 37) line 2. >> t/Annotation/Annotation......................NOK 9/159 >> # ? Failed test 'default itext' >> # ? at t/Annotation/Annotation.t line 307. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> >> # ? Failed test 'itext' >> # ? at t/Annotation/Annotation.t line 315. >> # ? ? ? ? ? ? ? ? ? 'ARRAY(0x100c02a48)' >> # ? ? doesn't match '(?-xism:Name: CALM1)' >> Can't locate object method "tagformat" via package "Bio::Annotation::TagTree" at t/Annotation/Annotation.t line 316. >> # Looks like you planned 159 tests but only ran 119. >> # Looks like you failed 3 tests of 119 run. >> # Looks like your test died just after 119. >> t/Annotation/Annotation......................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 9, 117, 119-159 >> ? ? ? ?Failed 43/159 tests, 72.96% okay (less 7 skipped tests: 109 okay, 68.55%) >> t/Annotation/AnnotationAdaptor...............ok >> t/Assembly/Assembly..........................ok 1/51 >> # ? Failed (TODO) test at t/Assembly/Assembly.t line 35. >> t/Assembly/Assembly..........................ok >> t/Assembly/ContigSpectrum....................ok >> t/Biblio/Biblio..............................ok >> ? ? ? ?1/24 skipped: various reasons >> t/Biblio/References..........................ok >> t/Biblio/biofetch............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Biblio/eutils..............................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/ClusterIO/ClusterIO........................ok >> ? ? ? ?8/12 skipped: various reasons >> t/ClusterIO/SequenceFamily...................ok 1/19Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/ClusterIO/SequenceFamily.t:16 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/ClusterIO/SequenceFamily.t line 19. >> # Looks like you planned 19 tests but only ran 2. >> # Looks like your test died just after 2. >> t/ClusterIO/SequenceFamily...................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 3-19 >> ? ? ? ?Failed 17/19 tests, 10.53% okay >> 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 >> ? ? ? ?11/279 skipped: various reasons >> t/LocalDB/BlastIndex.........................ok >> t/LocalDB/DBFasta............................ok >> t/LocalDB/DBQual.............................ok >> t/LocalDB/Flat...............................ok 1/24Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::DB::Flat::BinarySearch::get_Seq_by_id Bio/DB/Flat/BinarySearch.pm:338 >> STACK: t/LocalDB/Flat.t:89 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at Bio/DB/Flat/BinarySearch.pm line 346. >> # Looks like you planned 24 tests but only ran 14. >> # Looks like your test died just after 14. >> t/LocalDB/Flat...............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 15-24 >> ? ? ? ?Failed 10/24 tests, 58.33% okay >> t/LocalDB/Index..............................ok 1/64Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: Bio::Index::AbstractSeq::_get_SeqIO_object Bio/Index/AbstractSeq.pm:163 >> STACK: Bio::Index::AbstractSeq::fetch Bio/Index/AbstractSeq.pm:127 >> STACK: t/LocalDB/Index.t:91 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "_fh" on an undefined value at Bio/Index/AbstractSeq.pm line 128. >> # Looks like you planned 64 tests but only ran 31. >> # Looks like your test died just after 31. >> t/LocalDB/Index..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 32-64 >> ? ? ? ?Failed 33/64 tests, 48.44% okay >> t/LocalDB/Registry...........................ok >> ? ? ? ?9/14 skipped: various reasons >> t/LocalDB/SeqFeature.........................ok >> t/LocalDB/transfac_pro.......................ok >> t/Map/Cyto...................................ok >> t/Map/Linkage................................ok >> t/Map/Map....................................ok >> ? ? ? ?19/267 skipped: various reasons >> 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 >> ? ? ? ?10/14 skipped: various reasons >> t/Matrix/SiteMatrix..........................ok >> t/Ontology/GOterm............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/GraphAdaptor......................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/go.............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/IO/interpro.......................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/Ontology/IO/obo............................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Ontology..........................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/OntologyEngine....................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/OntologyStore.....................skipped >> ? ? ? ?all skipped: The optional module Graph (or dependencies thereof) was not installed >> t/Ontology/Relationship......................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/RelationshipType..................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Ontology/Term..............................skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Perl.......................................ok >> ? ? ? ?10/29 skipped: various reasons >> 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..................................ok >> t/PopGen/Coalescent..........................ok >> t/PopGen/HtSNP...............................ok >> t/PopGen/MK..................................ok >> ? ? ? ?4/46 skipped: various reasons >> t/PopGen/PopGen..............................ok >> t/PopGen/PopGenSims..........................ok >> t/PopGen/TagHaplotype........................ok >> t/RemoteDB/BioFetch..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/CUTG..............................ok >> ? ? ? ?14/37 skipped: various reasons >> t/RemoteDB/DB................................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EMBL..............................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/EUtilities........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/HIV/HIV...........................ok >> ? ? ? ?13/30 skipped: various reasons >> t/RemoteDB/HIV/HIVAnnotProcessor.............ok >> t/RemoteDB/HIV/HIVQuery......................ok >> ? ? ? ?10/41 skipped: various reasons >> t/RemoteDB/HIV/HIVQueryHelper................ok >> t/RemoteDB/RefSeq............................ok >> ? ? ? ?10/16 skipped: various reasons >> t/RemoteDB/SeqHound..........................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqRead_fail......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/RemoteDB/SeqVersion........................ok >> ? ? ? ?8/10 skipped: various reasons >> t/RemoteDB/Taxonomy..........................skipped >> ? ? ? ?all skipped: The optional module XML::Twig (or dependencies thereof) was not installed >> t/Restriction/Analysis.......................ok >> t/Restriction/Gel............................ok >> t/Restriction/IO.............................ok 1/18 >> # ? Failed (TODO) test at t/Restriction/IO.t line 31. >> t/Restriction/IO.............................ok >> ? ? ? ?3/18 skipped: various reasons >> t/Root/Exception.............................ok >> t/Root/RootI.................................ok >> t/Root/RootIO................................ok >> ? ? ? ?2/31 skipped: various reasons >> t/Root/Storable..............................ok >> t/Root/Tempfile..............................ok >> t/Root/Utilities.............................ok >> t/SearchDist.................................skipped >> ? ? ? ?all 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.............................ok 1/1093 >> # ? Failed (TODO) test at t/SearchIO/blast.t line 527. >> # ? ? '0.852' >> # ? ? ? ? > >> # ? ? '0.9' >> >> # ? Failed (TODO) test at t/SearchIO/blast.t line 528. >> # ? ? '1.599' >> # ? ? ? ? <= >> # ? ? '1' >> t/SearchIO/blast.............................ok >> t/SearchIO/blast_pull........................ok 1/289 >> # ? Failed (TODO) test at t/SearchIO/blast_pull.t line 260. >> # ? ? ? ? ?got: '0.946' >> # ? ? expected: '0.943' >> t/SearchIO/blast_pull........................ok >> t/SearchIO/blasttable........................ok >> t/SearchIO/blastxml..........................ok 1/298 >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 258. >> # ? ? ? ? ?got: undef >> # ? ? expected: '31984247' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 259. >> # ? ? ? ? ?got: undef >> # ? ? expected: '88780' >> >> # ? Failed (TODO) test at t/SearchIO/blastxml.t line 260. >> # ? ? ? ? ?got: undef >> # ? ? expected: '49' >> t/SearchIO/blastxml..........................ok >> t/SearchIO/cross_match.......................ok >> t/SearchIO/erpin.............................ok >> t/SearchIO/exonerate.........................ok >> ? ? ? ?4/45 skipped: various reasons >> 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...........................ok 1/116 >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 45. >> # ? ? ? ? ?got: 'Bio::Location::Simple=HASH(0x100838ce8)' >> # ? ? expected: undef >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t line 284. >> # ? ? ? ? ?got: '\-\.=~' >> # ? ? expected: '-\?' >> >> # ? Failed (TODO) test at t/Seq/LocatableSeq.t 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 >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature......................ok >> ? ? ? ?7/214 skipped: various reasons >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> t/SeqIO......................................ok >> t/SeqIO/Handler..............................ok 1/550Bio::SeqIO: gbdriver cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::gbdriver. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> BEGIN failed--compilation aborted at Bio/SeqIO/Handler/GenericRichSeqHandler.pm line 140. >> Compilation failed in require at Bio/SeqIO/gbdriver.pm line 145. >> BEGIN failed--compilation aborted at Bio/SeqIO/gbdriver.pm line 145. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqIO/Handler.t:20 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "verbose" on an undefined value at t/SeqIO/Handler.t line 23. >> # Looks like you planned 550 tests but only ran 1. >> # Looks like your test died just after 1. >> t/SeqIO/Handler..............................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 2-550 >> ? ? ? ?Failed 549/550 tests, 0.18% okay >> t/SeqIO/MultiFile............................ok >> t/SeqIO/Multiple_fasta.......................ok >> t/SeqIO/SeqBuilder...........................ok >> t/SeqIO/Splicedseq...........................ok >> t/SeqIO/abi..................................skipped >> ? ? ? ?all 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..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/asciitree............................ok >> t/SeqIO/bsml.................................skipped >> ? ? ? ?all skipped: The optional module XML::DOM (or dependencies thereof) was not installed >> t/SeqIO/bsml_sax.............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/chadoxml.............................ok >> t/SeqIO/chaos................................ >> # ? Failed test 'use Bio::SeqIO::chaos;' >> # ? at t/SeqIO/chaos.t line 15. >> # ? ? Tried to use 'Bio::SeqIO::chaos'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/SeqIO/chaos.pm line 132. >> # BEGIN failed--compilation aborted at t/SeqIO/chaos.t line 15. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> # Looks like you failed 1 test of 8. >> t/SeqIO/chaos................................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED test 1 >> ? ? ? ?Failed 1/8 tests, 87.50% okay >> t/SeqIO/chaosxml.............................skipped >> ? ? ? ?all skipped: The optional module Data::Stag (or dependencies thereof) was not installed >> t/SeqIO/ctf..................................skipped >> ? ? ? ?all skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed >> t/SeqIO/embl.................................ok >> t/SeqIO/entrezgene...........................skipped >> ? ? ? ?all skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed >> t/SeqIO/excel................................skipped >> ? ? ? ?all skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed >> t/SeqIO/exp..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/gcg..................................ok 1/17 >> # ? Failed (TODO) test 'primary_id' >> # ? at t/SeqIO/gcg.t line 54. >> # ? ? ? ? ?got: 'Bio::PrimarySeq=HASH(0x100830bd0)' >> # ? ? expected: 'roa1_drome' >> t/SeqIO/gcg..................................ok >> t/SeqIO/genbank..............................ok >> t/SeqIO/interpro.............................skipped >> ? ? ? ?all 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 >> ? ? ? ?all 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 >> ? ? ? ?all 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..................................ok 1/59 >> # ? Failed (TODO) test 'accuracies' >> # ? at t/SeqIO/scf.t line 78. >> # ? ? ? ? ?got: 'ARRAY(0x100ac5648)' >> # ? ? expected: '482' >> t/SeqIO/scf..................................ok >> t/SeqIO/strider..............................skipped >> ? ? ? ?all skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed >> t/SeqIO/swiss................................ >> # ? Failed test 'use Bio::SeqIO::swiss;' >> # ? at t/SeqIO/swiss.t line 12. >> # ? ? Tried to use 'Bio::SeqIO::swiss'. >> # ? ? Error: ?Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> # BEGIN failed--compilation aborted at t/SeqIO/swiss.t line 12. >> # Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> # BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> # Compilation failed in require at (eval 14) line 2. >> # BEGIN failed--compilation aborted at (eval 14) line 2. >> Can't locate object method "new" via package "Bio::SeqIO" at t/SeqIO/swiss.t line 17. >> # Looks like you planned 240 tests but only ran 1. >> # Looks like you failed 1 test of 1 run. >> # Looks like your test died just after 1. >> t/SeqIO/swiss................................dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-240 >> ? ? ? ?Failed 240/240 tests, 0.00% okay >> t/SeqIO/tab..................................ok >> t/SeqIO/table................................ok >> ? ? ? ?112/450 skipped: various reasons >> t/SeqIO/tigr.................................ok >> t/SeqIO/tigrxml..............................skipped >> ? ? ? ?all skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed >> t/SeqIO/tinyseq..............................skipped >> ? ? ? ?all skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed >> t/SeqIO/ztr..................................skipped >> ? ? ? ?all 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 1/49Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/SeqTools/GuessSeqFormat.t:62 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> t/SeqTools/GuessSeqFormat....................NOK 25/49 >> # ? Failed test 'Can't call method "next_seq" on an undefined value at t/SeqTools/GuessSeqFormat.t line 64. >> # ' >> # ? at t/SeqTools/GuessSeqFormat.t line 71. >> # ? ? ? ? ?got: '0' >> # ? ? expected: '1' >> # Looks like you planned 49 tests but ran 1 extra. >> # Looks like you failed 1 test of 50 run. >> t/SeqTools/GuessSeqFormat....................dubious >> ? ? ? ?Test returned status 1 (wstat 256, 0x100) >> DIED. FAILED tests 25, 50 >> ? ? ? ?Failed 2/49 tests, 95.92% okay (less 2 skipped tests: 45 okay, 91.84%) >> t/SeqTools/OddCodes..........................ok >> t/SeqTools/SeqPattern........................ok >> t/SeqTools/SeqStats..........................ok >> t/SeqTools/SeqUtils..........................ok >> t/SeqTools/SeqWords..........................ok >> t/Species....................................ok >> ? ? ? ?5/21 skipped: various reasons >> t/Structure/IO...............................ok >> t/Structure/Structure........................ok >> t/Symbol.....................................ok >> t/TaxonTree..................................skipped >> ? ? ? ?all 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 >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Domcut..............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/ELM.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/GOR4................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/HNN.................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Mitoprot............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/NetPhos.............skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Analysis/Protein/Scansite............ok 1/14Bio::SeqIO: swiss cannot be found >> Exception >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Failed to load module Bio::SeqIO::swiss. Can't locate Data/Stag.pm in @INC (@INC contains: t/lib . /Users/carrieomalley/BioPerl-1.6.0/blib/lib /Users/carrieomalley/BioPerl-1.6.0/blib/arch /Users/carrieomalley/BioPerl-1.6.0 /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0) at Bio/Annotation/TagTree.pm line 112. >> BEGIN failed--compilation aborted at Bio/Annotation/TagTree.pm line 112. >> Compilation failed in require at Bio/SeqIO/swiss.pm line 197. >> BEGIN failed--compilation aborted at Bio/SeqIO/swiss.pm line 197. >> Compilation failed in require at Bio/Root/Root.pm line 420. >> >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422 >> STACK: Bio::SeqIO::_load_format_module Bio/SeqIO.pm:551 >> STACK: Bio::SeqIO::new Bio/SeqIO.pm:372 >> STACK: t/Tools/Analysis/Protein/Scansite.t:23 >> ----------------------------------------------------------- >> >> For more information about the SeqIO system please see the SeqIO docs. >> This includes ways of checking for formats at compile time, not run time >> Can't call method "next_seq" on an undefined value at t/Tools/Analysis/Protein/Scansite.t line 27. >> # Looks like you planned 14 tests but only ran 4. >> # Looks like your test died just after 4. >> t/Tools/Analysis/Protein/Scansite............dubious >> ? ? ? ?Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 5-14 >> ? ? ? ?Failed 10/14 tests, 28.57% okay >> t/Tools/Analysis/Protein/Sopma...............ok >> ? ? ? ?12/16 skipped: various reasons >> 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 >> ? ? ? ?all 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......................skipped >> ? ? ? ?all skipped: Network tests have not been requested >> t/Tools/Run/StandAloneBlast..................ok >> ? ? ? ?12/45 skipped: various reasons >> 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 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 >> ? ? ? ?all skipped: The optional module Set::Scalar (or dependencies thereof) was not installed >> t/Tree/Node..................................ok >> t/Tree/PhyloNetwork/Factory..................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/GraphViz.................skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/MuVector.................ok >> t/Tree/PhyloNetwork/PhyloNetwork.............skipped >> ? ? ? ?all skipped: The optional module Graph::Directed (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/RandomFactory............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/PhyloNetwork/TreeFactory..............skipped >> ? ? ? ?all skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed >> t/Tree/RandomTreeFactory.....................ok >> t/Tree/Tree..................................ok >> t/Tree/TreeIO................................ok >> ? ? ? ?2/74 skipped: various reasons >> t/Tree/TreeIO/lintree........................ok >> t/Tree/TreeIO/newick.........................ok >> t/Tree/TreeIO/nexus..........................ok >> t/Tree/TreeIO/nhx............................ok >> t/Tree/TreeIO/phyloxml.......................ok >> t/Tree/TreeIO/svggraph.......................ok >> ? ? ? ?3/4 skipped: various reasons >> 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 >> ? ? ? ?15/26 skipped: various reasons >> Failed Test ? ? ? ? ? ? ? ? ? ? ? ? Stat Wstat Total Fail ?List of Failed >> ------------------------------------------------------------------------------- >> t/AlignIO/AlignIO.t ? ? ? ? ? ? ? ? ?255 65280 ? ?28 ? 42 ?8-28 >> t/AlignIO/arp.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? ?48 ? 92 ?3-48 >> t/Annotation/Annotation.t ? ? ? ? ? ?255 65280 ? 159 ? 83 ?9 117 119-159 >> t/ClusterIO/SequenceFamily.t ? ? ? ? 255 65280 ? ?19 ? 34 ?3-19 >> t/LocalDB/Flat.t ? ? ? ? ? ? ? ? ? ? 255 65280 ? ?24 ? 20 ?15-24 >> t/LocalDB/Index.t ? ? ? ? ? ? ? ? ? ?255 65280 ? ?64 ? 66 ?32-64 >> t/SeqIO/Handler.t ? ? ? ? ? ? ? ? ? ?255 65280 ? 550 1098 ?2-550 >> t/SeqIO/chaos.t ? ? ? ? ? ? ? ? ? ? ? ?1 ? 256 ? ? 8 ? ?1 ?1 >> t/SeqIO/swiss.t ? ? ? ? ? ? ? ? ? ? ?255 65280 ? 240 ?479 ?1-240 >> t/SeqTools/GuessSeqFormat.t ? ? ? ? ? ?1 ? 256 ? ?49 ? ?2 ?25 50 >> t/Tools/Analysis/Protein/Scansite.t ?255 65280 ? ?14 ? 20 ?5-14 >> 57 tests and 313 subtests skipped. >> Failed 11/318 test scripts. 970/17228 subtests failed. >> Files=318, Tests=17228, 123 wallclock secs (88.54 cusr + 11.43 csys = 99.97 CPU) >> Failed 11/318 test programs. 970/17228 subtests failed. >> Carrie-OMalleys-MacBook-Pro:BioPerl-1.6.0 carrieomalley$ ./Build install >> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS >> Deleting blib/script/bp_sreformat.PLS.bak >> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl >> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS >> Deleting blib/script/seqconvert.PLS.bak >> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl >> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS >> Deleting blib/script/parse_hmmsearch.PLS.bak >> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl >> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS >> Deleting blib/script/bp_seqret.PLS.bak >> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl >> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS >> Deleting blib/script/tree2pag.PLS.bak >> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl >> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS >> Deleting blib/script/meta_gff.PLS.bak >> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl >> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS >> Deleting blib/script/nexus2nh.PLS.bak >> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl >> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS >> Deleting blib/script/filter_search.PLS.bak >> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS >> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl >> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS >> Deleting blib/script/generate_histogram.PLS.bak >> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl >> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS >> Deleting blib/script/heterogeneity_test.PLS.bak >> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl >> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS >> Deleting blib/script/flanks.PLS.bak >> blib/script/flanks.PLS -> blib/script/bp_flanks.pl >> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS >> Deleting blib/script/split_seq.PLS.bak >> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl >> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS >> Deleting blib/script/load_gff.PLS.bak >> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl >> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS >> Deleting blib/script/biogetseq.PLS.bak >> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl >> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS >> Deleting blib/script/bp_fetch.PLS.bak >> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl >> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS >> Deleting blib/script/mutate.PLS.bak >> blib/script/mutate.PLS -> blib/script/bp_mutate.pl >> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS >> Deleting blib/script/process_sgd.PLS.bak >> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl >> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS >> Deleting blib/script/bp_index.PLS.bak >> blib/script/bp_index.PLS -> blib/script/bp_index.pl >> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS >> Deleting blib/script/dbsplit.PLS.bak >> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl >> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS >> Deleting blib/script/oligo_count.PLS.bak >> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS >> Deleting blib/script/bp_seqfeature_load.PLS.bak >> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl >> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS >> Deleting blib/script/process_gadfly.PLS.bak >> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl >> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS >> Deleting blib/script/hmmer_to_table.PLS.bak >> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl >> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS >> Deleting blib/script/fastam9_to_table.PLS.bak >> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl >> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS >> Deleting blib/script/biofetch_genbank_proxy.PLS.bak >> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl >> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS >> Deleting blib/script/seq_length.PLS.bak >> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl >> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS >> Deleting blib/script/extract_feature_seq.PLS.bak >> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl >> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS >> Deleting blib/script/genbank2gff.PLS.bak >> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl >> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS >> Deleting blib/script/taxid4species.PLS.bak >> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl >> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS >> Deleting blib/script/bulk_load_gff.PLS.bak >> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl >> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS >> Deleting blib/script/search2gff.PLS.bak >> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl >> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS >> Deleting blib/script/blast2tree.PLS.bak >> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl >> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS >> Deleting blib/script/make_mrna_protein.PLS.bak >> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl >> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS >> Deleting blib/script/unflatten_seq.PLS.bak >> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl >> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS >> Deleting blib/script/search2tribe.PLS.bak >> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl >> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS >> Deleting blib/script/bioflat_index.PLS.bak >> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl >> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS >> Deleting blib/script/bp_seqfeature_delete.PLS.bak >> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl >> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS >> Deleting blib/script/query_entrez_taxa.PLS.bak >> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl >> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS >> Deleting blib/script/pairwise_kaks.PLS.bak >> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl >> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS >> Deleting blib/script/fast_load_gff.PLS.bak >> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl >> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS >> Deleting blib/script/chaos_plot.PLS.bak >> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl >> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS >> Deleting blib/script/taxonomy2tree.PLS.bak >> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl >> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS >> Deleting blib/script/bp_mrtrans.PLS.bak >> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl >> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS >> Deleting blib/script/search2alnblocks.PLS.bak >> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl >> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS >> Deleting blib/script/download_query_genbank.PLS.bak >> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl >> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS >> Deleting blib/script/bp_nrdb.PLS.bak >> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl >> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS >> Deleting blib/script/mask_by_search.PLS.bak >> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl >> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS >> Deleting blib/script/gccalc.PLS.bak >> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl >> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS >> Deleting blib/script/composite_LD.PLS.bak >> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl >> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS >> Deleting blib/script/classify_hits_kingdom.PLS.bak >> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl >> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS >> Deleting blib/script/aacomp.PLS.bak >> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl >> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS >> Deleting blib/script/process_wormbase.PLS.bak >> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl >> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS >> Deleting blib/script/local_taxonomydb_query.PLS.bak >> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl >> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS >> Deleting blib/script/biblio.PLS.bak >> blib/script/biblio.PLS -> blib/script/bp_biblio.pl >> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS >> Deleting blib/script/seqretsplit.PLS.bak >> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl >> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS >> Deleting blib/script/remote_blast.PLS.bak >> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl >> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS >> Deleting blib/script/genbank2gff3.PLS.bak >> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl >> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS >> Deleting blib/script/search2table.PLS.bak >> blib/script/search2table.PLS -> blib/script/bp_search2table.pl >> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS >> Deleting blib/script/search2BSML.PLS.bak >> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl >> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS >> Deleting blib/script/translate_seq.PLS.bak >> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl >> Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 >> Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 >> Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 >> Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 >> Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 >> Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 >> Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 >> Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 >> Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 >> Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 >> Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 >> Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 >> Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 >> Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 >> Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 >> Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 >> Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 >> Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 >> Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 >> Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 >> Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 >> Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 >> Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 >> Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 >> Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 >> Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 >> Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 >> Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 >> Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 >> Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 >> Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 >> Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 >> Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 >> Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 >> Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 >> Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 >> Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 >> Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 >> Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 >> Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 >> Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 >> Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 >> Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 >> Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 >> Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 >> Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 >> Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 >> Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 >> Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 >> Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 >> Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 >> Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 >> Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 >> Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 >> Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 >> Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 >> Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 >> Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Can't create '/usr/local/bin' >> mkdir /usr/local/bin: Permission denied at /System/Library/Perl/5.10.0/ExtUtils/Install.pm line 479 >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ?at /Users/carrieomalley/BioPerl-1.6.0/Bio/Root/Build.pm line 902 >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/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 sdshlxh at gmail.com Fri Jul 30 17:14:23 2010 From: sdshlxh at gmail.com (Ping Yao) Date: Fri, 30 Jul 2010 12:14:23 -0500 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: please remove me from the list. From Kevin.M.Brown at asu.edu Fri Jul 30 17:29:25 2010 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Fri, 30 Jul 2010 10:29:25 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 In-Reply-To: References: Message-ID: <1A4207F8295607498283FE9E93B775B406D682E2@EX02.asurite.ad.asu.edu> You can remove yourself by following the link at the bottom of every email. -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ping Yao Sent: Friday, July 30, 2010 10:14 AM To: bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Bioperl-l Digest, Vol 87, Issue 41 please remove me from the list. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From robfsouza at gmail.com Sat Jul 31 20:56:49 2010 From: robfsouza at gmail.com (Robson de Souza) Date: Sat, 31 Jul 2010 16:56:49 -0400 Subject: [Bioperl-l] SOAP Eutilities Message-ID: Hi, Bio::DB::SoapEUtilities, referred in the HOWTO on EUtilities, seems to have disappeared from the Git repository. A simple git clone git://github.com/bioperl/bioperl-live.git does not download it. Any ideas why? Robson